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Affymetrix® Data Exchange Console 2.0 User's Guide

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1. Save Cancel Figure 3 10 Review Conflicts The window displays a list of conflicts with the following information Status Icon Indicator of the status of the import No conflicts or conflicts resolved AP Unresolvable conflict files will be imported on a file by file basis 9 Error condition no files will be imported Experiment Name of imported experiment Items Particular file causing problem DAT template etc Conflict Description of the problem Description Override Resolution automatically selected Action Override Enter a new name for the file to override the automatically created name 3 Enter new names in the Override column if desired 4 Click Save to close the Review Conflicts window and enter the new file names 5 Click View Errors to review files that cannot be imported at all The View Errors window opens Figure 3 11 ced View Errors Experiment Data Name Data Type Error T BEDEW N UsersetMaskA Sample Unable to find the master file for the GCOS probe array type Hu6800 UsersetMask4 UsersetMaskA DAT Data Data file UsersetMaskA DAT cannot be transferred because the associated experiment UsersetMaskA cannot be transferred UsersetMaskA UsersetMaskA dup DAT Data Data file UsersetMask4_dup DAT cannot be transferred because the associated experiment UsersetMask4 cannot be transfered UsersetMask4 UsersetMask4 CEL Data Data file UsersetMask4 CEL
2. To select a GCOS system 1 Entera server name in the Connect To box or Browse to the location of the server A Click the Browse button The Browse for Folder window opens Figure 3 15 ES Select a GCOS Server u Domains Eh AFFYMETRIK COM B AFFYMETRIX_COM ARBOURGROUP A BCS CALVINTEST CARNNET COMICS A CORP B CUBAWAYGAMES E25 BASE OFFICE ELKEM B ENGSCI UWO CA A EU EXPRESSWG v H H H H H t H H al et Ee E E E Figure 3 15 Browse for Folder window B Browse to the folder with the files to be imported C Click OK The server name appears in the Connect To box Figure 3 14 2 You can select an import option to limit the files on the GCOS server that are displayed in DEC e Exclude previously migrated files Find use filters to find experiments and types of data to import If you select this option the Filter window appears when you click Next Browse display all experiments on the GCOS server If you choose this option the Select Experiments window appears when you click Next 3 Click Next The appropriate window opens 24 Affymetrix Data Exchange Console 2 0 User s Guide Filtering the Experiments You can use this window to filter experiments displayed in the select experiments window Figure 3 16 E Affymetrix Data Exchange Console What kind of experiments would you like to find Use the filters below to find the f
3. 5 834 758 5 936 324 5 981 956 6 025 601 6 141 096 6 171 793 6 185 030 6 201 639 6 207 960 6 218 803 6 225 625 6 252 236 6 335 824 6 403 320 6 407 858 6 472 671 6 490 533 6 650 411 6 643 015 6 813 567 and other U S or foreign patents Software products may be covered by one or more of the following patents U S Patent Nos 5 733 729 5 795 716 5 974 164 6 066 454 6 090 555 6 185 561 6 188 783 6 223 127 6 228 593 6 229 911 6 242 180 6 308 170 6 361 937 6 420 108 6 484 183 6 505 125 6510 391 6 532 462 6 546 340 6 687 692 6 607 887 7 062 092 and other U S or foreign patents Fluidics stations Products may be covered by U S Patent No 6 114 122 6 287 850 6 391 623 6 422 249 and other U S or foreign patents AutoLoader products may be covered by one or more of the following patents U S Patent Nos 6 511 277 6 604 902 6 705 754 7 108 472 and other U S or foreign patents Copyright 2008 Affymetrix Inc All Rights Reserved Chapter 1 Welcome to the Data Exchange Console 1 Chapter 2 Chapter 3 Chapter 4 Chapter 5 TERE W TABLE OF CONTENTS EE EE L A Data Migration 49 kk kk kk KK K KIRI KI KI KIRI KI KI KIRI KI KI KIRI KI KIRI KI SADE KI KI KIRI de A 1 Conventions Used in This Guide YY KEK IY 2 RESOUICES 45 66 by 4 arda sl bk ie ae d d a a d te EE dna be i DR eR 3 Introduction to Data Migration 0000 cee ee
4. m Hi n tr P fi i j 4 peg i E Tei ji ymetri ie x Data Exchange Console 2 0 User s Guide P N 702571 Rev 3 For research use only Not for use in diagnostic procedures Trademarks Affymetrix AW 9 GeneChip HuSNP GenFlex Flying Objective CustomExpress CustomSeq NetAffx Tools To Take You As Far As Your Vision The Way Ahead Powered by Affymetrix GeneChip compatible Command Console and GeneTitan are trademarks of Affymetrix Inc All other trademarks are the property of their respective owners Limited License Notice Limited License Subject to the Affymetrix terms and conditions that govern your use of Affymetrix products Affymetrix grants you a non exclusive non transferable non sublicensable license to use this Affymetrix product only in accordance with the manual and written instructions provided by Affymetrix You understand and agree that except as expressly set forth in the Affymetrix terms and conditions that no right or license to any patent or other intellectual property owned or licensable by Affymetrix is conveyed or implied by this Affymetrix product In particular no right or license is conveyed or implied to use this Affymetrix product in combination with a product not provided licensed or specifically recommended by Affymetrix for such use Patents Scanner products may be covered by one or more of the following patents U S Patent Nos 5 578 832 5 631 734
5. cannot be transferred because the associated experiment UsersetMask4 cannot be transferred UsersetMaskA UsersetMaskA dup CEL Data Data file Ul sersetMask _dup CEL cannot be transferred because the associated experiment UsersetMaskA cannot be transferred UserselMaskA UsersetMaskA CHP Data Data file UsersetMaskA CHP cannot be transferred because the associated experiment LsersetMaskA cannot be transferred UsersetMask4 UsersetMask4_dup CHP Data Data file UsersetMask4_dup CHP cannot be transferred because the associated experiment LsersetMaskA cannot be transferred UsersetMaskA UsersetMaskA_dup_AbsMaskScaling CHP Data Data file UsersetMaskA_dup_AbsMaskScaling CHP cannot be transferred because the associated experiment LsersetMask cannot be transfered Figure 3 11 View Errors chapter 3 DEC Import 21 The window displays a list of files and data with the following information Experiment Name of imported experiment Data Name Particular file causing problem DAT template etc Data Type Type of file Error Reason the file cannot be imported Click Close in the View Error window 7 Click Import The Import Status window opens Figure 3 12 Tracking Import Status The Import Status window Figure 3 12 displays a list of the imported files with information about whether the import was successful or not B0 Affymetrix Data Exchange Console Ee ix Import Status Starting transfer
6. g Li En aia E TER L LI lt ad F n m aw dt 3 TT J 5 Li 4 te ono i m E N ERNA WELCOME TO THE DATA EXCHANGE CONSOLE This manual explains the process of migrating data from various versions of GeneChip Operating Software GCOS software into Affymetrix GeneChip Command Console AGCC software and back The migration is performed using the GCOS Data Transfer Tool DTT and the Affymetrix Data Exchange Console DEC The manual includes e A discussion of the differences between GCOS and AGCC see Chapter 2 Introduction to Data Migration on page 5 e Instructions on using the Data Exchange Console to import data into and export data from AGCC See Chapter 3 DEC Import on page 13 Chapter 4 DEC Export on page 37 e Descriptions of the possible impacts on data that may result see Chapter 5 Impacts on Data on page 47 The DEC Installation installs The Data Exchange Console install package installs e Data Exchange Console DEC e Affymetrix Command Console Library Importer Tool e Affymetrix Command Console Reconnector The installation of DEC and the other tools is described in the 4GCC 2 0 Installation Instructions The use of the Library Importer Tool is described in the AGCC 2 0 Installation Instructions The use of the Reconnector is described in the Affymetrix Command Console Reconnector 2 0 User s Guide See Affymetrix Data Transfer Tool User s Guide Version 1 1 for information
7. using path completion or A Click the Browse button The Browse for Folder window opens Figure 3 21 28 Affymetrix Data Exchange Console 2 0 User s Guide Browse For Folder Desktop amp B My Documents E 4 My Computer E a My Network Places g Recycle Bin E 7 06 KO AfFymetrix Downloads E K2 CNAT 401 E EZ GCOS Tech Notes Hauw m E Library K New Folder z Figure 3 21 Browse for Folder window B Browse to the folder with the files to be imported C Click OK A list of the available flat files is displayed in the box in the Select Files window Figure 3 22 Select Files Type the folder path or browse to the folder then selectthe files you wish to import You can change file associations by dragging and dropping nodes in the file tree The Sample ARR files are created by DEC during import Lookin C Test Data DEC_Test Files FlatFilelmpor Browse o D C Test Data DEC_Test_Files FlatFilelmport SIGH chip25 ARR o ME chip25 a m chip25 DAT MH chip25 CEL chip25 JPG ME DEC Test 3 with UsersetARR ME DEC Test 3 with Userset o jv DEC Test 3 with Userset DAT o M DEC Test 3 with Userset CEL DEC Test 3 with Userset CHP DEC Test 3 with Userset JPG o ME Exp with Template ARR BF Exp with Template Select All Unselect All Figure 3 22 files for selection Each flat file has a checkbox next to it The data files DAT CEL and CHP are grouped by file name and embed
8. 56 PM Subject 03 brain ARR 7 10 2007 12 41 16 PM Include DAT Data Figure 4 4 Select Data To select Sample ARR files 1 Select the files for export from the list You can also make and clear selections using the Select All and Unselect All buttons Deselect Include DAT data if you wish to exclude the DAT data from the export 3 Click Next The Select Location window opens chapter 4 DEC Export 41 Selecting a Location The Select Location window Figure 4 5 allows you to select the folder where the DTT file will be placed E Affymetrix Data Exchange Console Where would you like to save the new file s DTT Archive File Name Type the folder path and DTT file name or browse to the folder and enter the DTT file name Save to C Documents and Settings rallso Desktop 7 14 2007_085507_AGCCDTT Estimated Disk Space Required 5638 MB Space Available 16524 MB File Size Options Add Comments Check the box and select a maximum file size if you wish to split the archive into smaller files Create multiple files with max size no larger than Figure 4 5 Select Location To select a location for the exported files 1 Select the location and file name by typing the path and file name into the Location box using path completion or A Click the Browse button The Save As window opens Figure 4 6 Save in 3 Desktop v 3 e E El my Documents Iz 3 1 2007_111359_AGCC DTT ES if My Comp
9. Figure 3 3 Browse For Folder My Documents My Computer Ci ee Local Disk C O archive O Archive calvin Docs 03 16 O cache O Calvin Configurations O Calvin Docs O Calvin wG 3 Command_Console z amp E E E E E Figure 3 3 Browse for Folder window B Browse to the folder with the files to be imported C Click OK 16 Affymetrix Data Exchange Console 2 0 User s Guide A list of the available DTT or XML files is displayed in the box in the Select Files window Figure 3 4 Select Files Type the folder path or browse to the folder then selectthe DTT files you wish to import Lookin CATest Data DEC_Test Files Date O OTT 14 Expression DTT 2 6 2007 4 15 47 PM Select All Unselect All Figure 3 4 DTT or XML files for selection Each DTT or XML file has a checkbox next to it 2 Select the checkbox es for the file s you with to import You can also make and clear selections using the Select All and Unselect All buttons 3 Choose Import options Complete Import all experiments and data If you select this option the Select Save Location window see page 17 opens when you click Next Custom choose specific experiments to import If you select this option the Select Experiments window opens when you click Next 4 Click Next The appropriate window opens Selecting Experiments The Select Experiments window Figure 3 5 allow you to select individual experiments in
10. Sample1Array2 DAT File GUID Sample1Array2 DAT File GUID Sample1Array2 DAT File GUID Sample1Array2 Array GUID PSample1Array2 Array GUID Sample1Array2 Array GUID Sample1Array2 Array GUID Figure 2 3 GUIDs in Sample and Data Files During Sample registration the Sample file 1s assigned a Sample File GUID in addition an Array GUID is provided for every array name entered Every data file DAT CEL and CHP generated for an array will contain the Array GUID for the array as well as the GUIDs for each of its parent data files The GUIDs enable you to trace the lineage of any data file independent of the file name The parent child relationships can be broken under certain circumstances when using DEC see Affymetrix Command Console Reconnector User s Guide for information on repairing these broken links File Format Impacts There are differences in the way AGCC stores data as opposed to GCOS These differences can cause impacts when you copy data from one to the other The impacts may vary depending upon e Which way the transfer takes place GCOS to AGCC or AGCC to GCOS The software source for the data being imported MAS 5 x and the different versions of GCOS The type of file that is being transferred DAT CEL and CHP The array type expression reseq mapping etc The type of algorithm used for processing the data e Possibly the actual transfer file format used DTT CAB MAS 5 x You need to be aware of the pos
11. These subfolders are added to their respective projects in AGCC When data is imported from GCOS the userset information on analysis algorithm parameters is kept in Parameter Files PARAM These files are not visible in the AGCC interface Template information is placed into a template file that can be edited through the AGCC Portal See Chapter 2 Getting Started With 4GCC on page 5 of the AGCC User s Guide for more information about the file types and data organization n AGCC Tracking Files with GUIDs A GUID or Globally Unique Identifier is assigned to each file for tracking Figure 2 3 GUIDs are numbers generated to track a file that will be unique to that file chapter 2 Introduction to Data Migration 9 Sample ARR File Image DAT File s Ed Intensity CEL File s Probe Intensity CHP File s File Name Sample1 ARR Sample ARR File GUID File Name Sample1Array1 CHP File Name Sample1Array1 CEL Sample1Array1 CHP File GUID File Name Sample1Array1 DAT Sample1Array1 CEL File GUID Sample1Array1 CEL File GUID Array Name Sample1 Array Sample1Array1 DAT File GUID Sample1Array1 DAT File GUID Sample1Array1 DAT File GUID sample1Array1 Array GUID Sample1Array1 Array GUID Sample1Array1 Array GUID Sample1Array1 Array GUID File Name Sample1Array2 CHP o File Name Sample1Array2 CEL Sample Array2 CHP File GUID File Name Sample1Array2 DAT Sample1Array2 CEL File GUID Sample 1Array2 CEL File GUID Array Name Sample1Array2
12. by Project e Sample Experiment Sample and Experiment Templates are used to organize the attributes and their data characteristics the templates can be selected for a sample or experiment during registration Templates can be edited to add or remove attributes or change their data characteristics The GCOS database also stores algorithm settings for the different types of analysis expression mapping etc These settings are organized into usersets which can also be copied and edited AGCC Files When GCOS data is transferred into AGCC the sample and experiment attributes and other information are placed in the following XML files Sample files ARR Audit Information files AUDIT The experiment data is stored in DAT Files CEL files CHP files e MSK files These files contain the same type of data as their counterparts in GCOS but the format is different and some data may not be included 8 Affymetrix Data Exchange Console 2 0 User s Guide H Sample File Sample ARR With Sample Attributes Array name SecondArray used forDAT CEL and CHP files E DAT File FirstArray DAT E DAT File SecondArray DAT L E CEL File FirstArray CEL g Ed CEL File SecondArray CEL CHP File FirstArray CHP CHP File SecondArray CHP Figure 2 2 Sample File with multiple arrays The files can be assigned to a Project during import or you can create subfolders to preserve the GCOS project structure
13. clear selections using the Select All and Unselect All buttons 3 Move arrays and data files from one sample file to another if necessary to get the relationships between files correct For example if you have run duplicate arrays for a sample in GCOS Figure 3 25 the duplicate arrays will be initially set up with separate array names and Sample files LEI chip25ARR H J DEC Test 3 with UsersetARR H J Exp with Template ARF ml MASS AFR 7 EN UsersetMaskA ARR eG UsersetMaskA p jv UsersetMaskA dat Er Er Erl Er S A UsersetMaskA CEL M UsersethaskA CHP ersetiiaska dup ARR 2 7IEN Usersettiask4_dup 27 58 UsersetMaskA dup CEL VES UsersetMaskA_dun CHP FI Usersetiiask4_dup2 CEL Figure 3 25 Duplicate arrays Y ou can consolidate the arrays under one Sample file by moving the duplicate array name and all its data files to the first Sample file Figure 3 26 30 Affymetrix Data Exchange Console 2 0 User s Guide TIEK DEC Test 3 with UsersetARR TIEF Exp with Template ARR ml MASS AFR Sata MEE SEER ARR BW UsersetMaskA 2 FI LisersetMaskA dat 2 7 LisersetMaskA CEL IE UsersethaskA CHP 2 jv Usersettiask4_dup FI UsersetMaskA_dup CEL IE UsersetMaskA_dup CHP FI UsersetMaskA_dup2 CEL DIE UsersetMaskA_dup ARR Figure 3 26 UsersetMaskA_dup moved to UsersetMaskA ARR sample file 4 Click Next The Select Location window opens Selecting a Location See Selecting a Location
14. file Error Reason the file cannot be exported 7 Click Close in the View Error window Click Export The Export Status window opens Figure 4 12 Export Status This window Figure 4 12 displays the status of the data export 46 Affymetrix Data Exchange Console 2 0 User s Guide E Affymetrix Data Exchange Console Export Status Converting file S1068100251923030604300127464495 DAT The list below shows the export status of each Sample ARR file Click in a rowto see more detail far that sample Experiment Message Build37EU133a File Build37EU133a ComProbeMask CHP was converted successfully 5105990040591 1030806400743887625 File 5105990040591 1030806400743887625 CEL was converted successfully 51068100251 9230306043001 27464485 File 51058100251323030504300127454485 CEL was converted successfully 51068100251 9230306043001 27464495 Converting file 51068100251 9230306043001 27464495 DAT 510681 002520030307043001 31568471 51 0681 002520030307043001 31568507 51130200457544061 3064009494501 47 52001 9003061 43070204300292035858 252001 90032074301 0605400001 129266 52005500451817101305401415533535 52006500461817101306401416533703 52006500461817101306401416533707 Subject D1 brain Subject 02 brain Subject_03_brain Figure 4 12 Export Status The window displays the following columns Status Icon Indicator of the status of the export No
15. of DAT Data Build37EU133a CI RR The list below shows the import status of each experiment Click in a row to see more detail for that experiment Experiment Message d Build37EU133a Starting transfer of DAT Data Build37EU133a Click View Errors to view the error log Figure 3 12 Import Status window The screen displays the following columns Status Icon Indicator of the status of the import No conflicts or conflicts resolved In progress 9 Unresolvable conflict error condition File will not be imported Experiment Name of imported experiment Message Particular file causing problem DAT template etc Click in a row to display the Detailed Migration Results window for the experiment being imported Figure 3 13 22 Affymetrix Data Exchange Console 2 0 User s Guide GE Detailed Migration Results for Plus2 Data Name Data Type Error Sample DAT Data CEL Data CHP Data Plus2_ComMaskScaling CHP Data Plus2_AbsNormM ask ji CHP Data Plus2_ComNormMask CHP Data Close Figure 3 13 Detailed Migration Results window The window lists the following information about the experiment Data Name Name of file Data Type Type of file being imported or created Error Brief description of the condition that cannot be resolved if any After the import is finished Click View Errors to view the error log or Click Start Again to import more files or Click Finish to clo
16. on using the DTT Data Migration You can perform a data migration e From GCOS to AGCC This allows you to transfer previously generated data into AGCC for organization and analysis e From 4GCC to GCOS This allows you to transfer data from AGCC to a computer with GCOS installed if you are dealing with a user who has not upgraded yet 2 Affymetrix Data Exchange Console 2 0 User s Guide From GCOS to AGCC You can migrate data between GCOS systems and AGCC systems using several different methods You can use the Data Transfer Tool DTT to export data from GCOS in one of the DTT file formats and then import the DTT files into AGCC using DEC This enables you to transfer experiment and sample information as well as the Data files DAT CEL and CHP You can connect directly between the GCOS system and the AGCC system using DTT This will also enable you to transfer experiment and sample information from the GCOS process database You can import the flat data files in MAS 5 x or GCOS 1 x formats into AGCC using DEC This will not import experiment and sample information For more information see Chapter 3 DEC Import on page 13 From AGCC to GCOS Y ou can migrate data from AGCC to GCOS by using DEC to export AGCC data into DTT format which can then be imported into a GCOS system This is useful when dealing with users who have not updated to AGCC yet For more information see Chapter 4 DEC Export on page 37 NOT
17. the DTT or XML files The list displays the following information Experiment Experiment name File Location DTT file name User User who created the sample in GCOS Date Date of file creation Assay Type General type of array Mapping e Expression Universal e Resequencing Probe Array Type Type of probe array analyzed You can sort the list order by clicking in the header of the column you wish to sort by E Affymetrix Data Exchange Console What experiments would you like to import Select Experiments Select the experiments you wish to import Assay Experiment File Location a User Date T ype chapter 3 DEC Import Probe Array Type Build37EU133a DTT 1 3 Expression DTT rmeyer 3 23 2005 Expression HG UT 334 DTT 1 3 Expression DTT rallso 6 9 2006 Expression HG UT 334 DTT 1 4 Expression DTT thoang 6 14 2006 Expression HG U133 Plus 2 DTT 1 4 Expression DTT thoang 3 17 2006 Expression HG U133 Plus 2 UsersetMaskA DTT 1 4 Expression DTT thoang 6 14 2006 Expression Select All Unselect All Import DAT data lf you wish to exclude DAT data uncheck the box below Include DAT data Figure 3 5 DTT Import Select Experiments To select experiments Hu6800 1 Select the checkbox es for the experiment s you with to import Y ou can also make and clear selections using the Select All and Unselect All buttons 2 Deselect Include DAT data i
18. 09 MB Space Available 53112 MB Figure 3 29 Review List displayed chapter 3 DEC Import 33 The Review list displays Figure 3 30 Import Select the checkbox to import the files for the array plate Details Click the Details button to display the Detailed Plate Results for dialog box Figure 3 33 Plate Name Unique Plate identifier as specified in GCOS DAT Number of DAT files to be imported standard number of DAT files for this array plate type CEL Number of CEL files to be imported standard number of CEL files for this array plate type CHP Number of CHP files to be imported can have multiple CHP files for a CEL file Message Additional information notice of problems etc Problems with the files are displayed in the list Step 2 Review list of files to be imported Import Details Plate Name CHP Message El ss00014037280112808226_032008_ 22 24 22 24 22 Some pegs do not have all the data Rela Estimated Disk Space Required 6287 MB Space Available 46953 ME Figure 3 30 Review List with Missing DAT and CEL files An estimate of the disk space required for import and the disk space availabe are displayed below the list If there are problems the file types that are incorrect are displayed in red and error messages are displayed Step 2 Review list of files to be imported Import r Plate Hame CHP Message v 550001 4037283112808226_ 022008 Duplicate 24 Duplicate 24 Duplicate Est
19. 5 98 98 EEO0014037283112808226 032008 HTHWS VV inhouse 24 2EO07 98 98 BEO0014037283112808226 032008 HTHWS VV inhouse 24 2E09 98 98 Figure 3 35 Detailed Plate Results window After the import is finished e Click Back to import more data or Click Finish to close the DEC window The imported data is visible in the Data folder RR HA More m WIN I O linn E E Chapter DEC EXPORT The DEC Export option allows you to export data in DTT format for use in a GCOS system DEC Export involves the following sets of steps Choosing How to Select Files for Export Using the Filter on page 38 Selecting Sample Files for Export on page 40 Selecting a Location on page 41 Reviewing Data and Fixing Conflicts on page 42 D M e WO SS Export Status on page 45 NOTE CHP files created with the new expression algorithms e g PLIER RMA iterPLIER and genotyping algorithms e g BRLMM P Birdseed cannot be loaded into GCOS and will not be included in the DTT file NOTE HT data from AGCC cannot be imported back into GCOS Choosing How to Select Files for Export You can select files to export e From a filtered set of Sample files e From a list of all the Sample files in the AGCC system The Export Options window Figure 4 1 allows you to choose whether to filter the list of files or not 38 Affymetrix Data Exchange Console 2 0 User s Guide Be Affymetrix Data
20. AT CEL headers The data is copied to the user provided folder To select an import method 1 Select the format in the list 2 Click Next The appropriate Select Data File window opens chapter 3 DEC Import Importing DTT Files DTT files are a GCOS interchange format created with the Data Transfer Tool they use an XML file to transfer the sample and experiment data for the DAT CEL and CHP data files When exporting data from GCOS in DTT format for import using DEC you can e Place the XML and data files into a zip file for easy transport e Transfer the separate XML and data files in flat file format Selecting Data File The Select File window Figure 3 2 allows you to select the DIT or XML files for import ES Affymetrix Data Exchange Console What DTT files would you like to import Select Files Type the folder path or browse to the folder then selectthe DTT files you wish to impart Look in CATest DatelDEC Test Files File Date C DTT 1 3 Expression DTT 2 6 2007 4 15 31 PM CI DTT 1 4 Expression DTT 2 6 2007 4 15 47 PM Select All Unselect All Choose Import Option Complete import all experiments and data Custom choose specific experiments to import Figure 3 2 Step 2 Select Files To select DTT or XML files for import 1 Select the location by typing the path into the Location box using path completion or A Click the Browse button The Browse for Folder window opens
21. DAT v1 DAT v2 Subgrids DATv2 Subgrids added added CEL file CEL v1 ASCII CEL v2 CEL v2 CEL v2 CEL v2 format Binary Version Binary Version Binary Version Binary Version CHP Expression CHP v1 CHP v2 CHP v3 XDA v1 CHP v3 XDA v1 CHP Universal CHP v1 CHP v2 CHP v3 XDA v1 CHP v3 XDA v1 CHP Mapping CHP v2 CHP v3 XDA v1 CHP v3 XDA v1 CHP v3 XDA v1 CHP CHP v2 CHP v3 XDA v1 CHP v3 XDA v1 CHP v4 XDA v2 Resequencing RPT RPT v1 Format used by DEC for output
22. E CHP files created with the new expression algorithms e g PLIER RMA iterPLIER and genotyping algorithms e g BRLMM P Birdseed cannot be loaded into GCOS and will not be included in the DTT file NOTE HT data from AGCC cannot be imported back into GCOS Conventions Used in This Guide Steps This manual provides a detailed outline for all tasks associated with the Data Exchange Console Various conventions are used throughout the manual to help illustrate the procedures described Explanations of these conventions are provided below Instructions for procedures are written in a step format Immediately following the step number is the action to be performed Following the response additional information pertaining to the step may be found and is presented in paragraph format For example 1 Click Yes to continue The Delete task proceeds In the lower right pane the status is displayed To view more information pertaining to the delete task right click Delete and select View Task Log from the shortcut menu that appears Font Styles Bold fonts indicate names of commands buttons options or titles within a dialog box When asked to enter specific information such input appears in italics within the procedure being outlined For example 1 Click the Find button or select Edit Find from the menu bar The Find dialog box appears 2 Enter AFF X BioB 5_at in the Find what box then click Find Next to view the first se
23. Exchange Console How would you like to select files for export Choose how vou would like to select files for export Select Export Option Find Pre filter the files you select from O Complete Select from all Sample ARR files Figure 4 1 Select Export Options To select an option 1 Select Find to filter the Sample files If you select this option the Filter window opens Complete to select from all sample files and data If you select this option the Select Sample Files window appears 2 Click Next The appropriate window opens Using the Filter The Filter window Figure 4 2 allows you to filter the Sample files that will be displayed in the Select Array files window Y ou can filter by Project e Dates that Sample ARR file or DAT files were created chapter 4 DEC Export 39 ES Affymetrix Data Exchange Console What kind of Sample ARR files would you like to find Step 1 Select Project s Select one or more projects to limit the search to those projects mn Alzheimer 1 Cancer 2 O Dr Moriarty C Plus2 C Build37EU133a Data C Dr Smith O Schizophrenia C Cancer C Default CO GCOS 1 3 Step 2 Select Date hange Filter by Sample Registration Date O Scan Date DAT file creation date Search Recent OR Specify a date range i u vol to Oo Figure 4 2 Data Filters To filter 1 Select a project from the Select Projects list 2 Select a Date Filter option Sample
24. G Data Build37EU133a_1 CEL CEL Data Build3 EU133a_1 CHP CHP Data Build37EU133a AbsMaskScaling 1 CHP CHP Data Build37EU133a_ComMaskScaling_1 CHP CHP Data Build37EU133a_ComProbeMask_1 CHP CHP Data Build37EU133a_AbsProbeMask_1 CHP CHP Data Figure 4 8 Detailed Validation Results The list displays the following information about the experiment Data Name Name of file Data Type Type of file being exported or created Error Brief description of the condition that cannot be resolved if any To review the data for export 1 Review the list for conflicts Conflicts will automatically be resolved but you can override the automatic resolution using the Review Conflicts window CHP files created with the new expression algorithms e g PLIER RMA iterPLIER and genotyping algorithms e g BRLMM_P Birdseed cannot be loaded into GCOS and will not be included in the DTT file If this happens the following notice appears Figure 4 9 Data Exchange Console Some CHP Files were removed From the export Please see the log file For more details Figure 4 9 CHP file removal notice 2 Click OK in the notice 3 Click the Review Conflicts button to override the automatic resolutions The Review Conflicts window opens Figure 4 10 aa Affymetrix Data Exchange Console 2 0 User s Guide EF Review Conflicts ve have found the following conflicts au may change the resolution by select
25. Log Displays a text file with a record of the file imports Cancel Close the dialog box Back Return to the previous step disabled in this window Next Go to the next step To import data 1 Select Import Data into Command Console from GCOS 2 Click Next The Select Import Method window opens see page 13 To export data 1 Select Export Data out of Command Console to a DTT file 2 Click Next The Select Export Options window opens see page 37 GCOS AGCC File Differences There are some differences between the way files are organized and the data is stored in AGCC and GCOS You need to understand these differences to understand some of the problems that may arise when importing or exporting data GCOS Files and Database In GCOS the sample and experiment information is kept in the process database as attributes of the sample and experiment The information is assigned by the user during experiment registration chapter 2 Introduction to Data Migration 7 The database includes information about the data files and about the fluidics and scanner operation The data generated during the experiment is in individual data files e Image DAT files Intensity CEL Files Probe Analysis CHP Files Report RPT Files The format of these file types may have changed in different versions of GCOS For more information see Impacts Caused by Migrating from GCOS to AGCC on page 47 The information and data are organized
26. NOTE This option is not available when importing MAS 5 x or GCOS flat files 3 Click Next The Review Data window opens Reviewing Data The Review Data window Figure 3 8 displays a list of the files to be imported with the following information Status Icon Indicator of the status of the import No conflicts or conflicts resolved AP Unresolvable conflict files will be imported on a file by file basis Error condition no files will be imported Sample AGCC Sample file name based on the GCOS Experiment name Type Type of data CEL DAT CHP GRD JPG Conflict Brief description of the conflict if any Resolution Automatic resolution to the conflict Error Description of a condition that cannot be resolved Items with errors are discarded on a file by file level CEL CHP etc chapter 3 DEC Import 19 BE Affymetrix Data Exchange Console EIER Review the data before you import it into Command Console Review the following items and click Import to begin importing the files To review all conflicts click Review Conflicts To see more detail for an experiment click the icon in the first column If there is an error with an experiment it cannot be imported Sample DAT CEL CHP JPG GRD Conflict Resolution Build37EU133a Barcode Used Barcode is already used in Command Console 5106810024720701110430000489 GCOS 1 3 Multiple 1 conflict was resolved and 1 conflict was not resolved in the experiment M
27. P Plus2 UsersetMaska Click to view and edit conflict resolutions Review Conflicts Click View Errors to review the error log Figure 3 8 DTT Import Review Data Conflicts arise because of discrepancies between the data in the different GCOS files being imported and between the data being imported and data already in AGCC Click in a row to display the Detailed Validation Results for the experiment being imported Figure 3 9 EE Detailed Validation Results for UsersetMaskA Sel Data Name Data Type Error UsersetMaskA Sample Unable to find the master file for the GCOS probe array type Hu6800 UsersetMaskA DAT Data Data file UsersetMask DAT cannot be transferred because the associated experiment UsersetMask4 cannot be transferred UsersetMask4_dup DAT Data Data file UsersetMask4_dup DAT cannot be transferred because the associated experiment UsersetMaskA cannot be transferred UsersetMaskA CEL Data Data file UsersetMask4 CEL cannot be transferred because the associated experiment UsersetMask4 cannot be transferred UsersetMask4_dup CEL Data Data file UsersetMaskA_dup CEL cannot be transferred because the associated experiment UsersetMask4 cannot be transferred UsersetM ask CHP Data Data file UsersetMaskA CHP cannot be transferred because the associated experiment LsersetMaskA cannot be transferred UsersetMask4_dup CHP Data Data file UsersetMaskA_dup CHP canno
28. Registration Date the Sample ARR file was created Date Scan Date Date the DAT file was created 3 Select a date or range of dates for file creation e Select a date limit from the Search Recent drop down box or A Click on the left hand date range box The checkbox is selected and a calendar for the current month appears Figure 4 3 specify a date range 3 20 2007 March 2007 Sun Mon Tue Wed Thu 1 4 5 a T a 11 12 13 14 16 18 18 E 21 22 25 26 oz 20 24 _ Today 3 20 2007 Figure 4 3 From Calendar B Select a date for the start of the range You can move from month to month by clicking the lt and gt buttons If you only select a start date the filter will display only the files created on or after that date To select a range of dates 40 Affymetrix Data Exchange Console 2 0 User s Guide e Select a date for the end of the range If you only select an end date the filter will display only the files created on or before that date 4 Clck Find The Select Sample Files window appears Selecting Sample Files for Export The Select Files window Figure 4 4 displays a list of Sample ARR files that can be exported Be Affymetrix Data Exchange Console What Sample ARR files would you like to export select Files Export DAT Data Name Date Created lf you wish to exclude DAT data Subject 01 brain ARR 7 10 2007 12 36 41 PM uncheck the box below Subject 02 brain ARR 7 10 2007 12 38
29. _032008_HTHWS_V_ _inhouse_24_2 C09 98 98 550001 40372831 12808226_032008_HTHWS_V_V_inhouse_24_2 D05 98 98 550001 40372831 12808226_032008_HTHWS_V_V_inhouse_24_2 D07 98 98 550001 40372831 12808226 032008 HTHWS VV inhouse 24 2DOS 98 98 550001 40372831 12808226_032008_HTHWS_V_V_inhouse_24_2 E05 98 98 550001 40372831 12808226_032008_HTHWS_V__inhouse_24_2 E07 98 98 550001 4037283112808226_032008_HTHw S__Y_inhouse_24_2 E03 98 98 Close Figure 3 33 Detailed Plate Results dialog box for duplicate peg info The dialog box displays Samples Name for Sample ARR file to be created mini DAT Number of mini DAT files to be imported for the array number of mini DAT files that are standard for the array plate type CEL Number of CEL files to be imported CHP Number of CHP files Message Additional information notice of problems etc 5 Review the data to be imported and click the Import button The import begins and the Import Progress window opens Figure 3 34 chapter 3 DEC Import 35 Import Progress The Import Status window Figure 3 34 displays a list of the imported files with information about whether the import was successful or not E Affymetrix Data Exchange Console Importing data 23 pegis out of 24 pegis remaining to be imported BE Details Plate Name Peg Imported Message SS Evil AAI NN NN Cancel Figure 3 34 Import Progress The scre
30. ample ARR file for each group of data files DEC will group data files using file names and embedded parent file information and you can change the grouping if necessary to accommodate special circumstances Selecting Data File The Select File window Figure 3 20 allows you to select the data files for import Be Affymetrix Data Exchange Console What experiments and data would you like to import Select Files Type the folder path or browse to the folder then select the files you wish to import You can change file associations by dragging and dropping nodes in the file tree The Sample ARR files are created by DEC during import Lookin CATestDatelDEC Test FilestFlatFilelmpont A a ME chip25 ARR a mE chip25 2 98 chip25 DAT Mi chip25 CEL chip25 JPG o ME DEC Test 3 with UsersetARR ME DEC Test 3 with Userset s v DEC Test 3 with Userset DAT A DEC Test 3 with Userset CEL DEC Test 3 with Userset CHP DEC Test 3 with Userset JPG amp MBF Exp with Template ARR SBF Exp with Template Select All Unselect All Figure 3 20 Select File The page displays a list of the available files in a hierarchical tree The Data files are arranged in groups based on the file names and the embedded parent file information It also displays the Sample file and Array Name s that will be created for the files in AGCC To select files for import 1 Select the location by typing the path into the Location box
31. anization between GCOS and AGCC may cause impacts to the data being copied The particular impacts depend upon the type of data being transferred When you copy data from GCOS to AGCC the following files and data may be impacted DAT Files on page 48 CEL Files on page 48 CHP Files on page 49 Sample Data on page 49 Experiment Data on page 49 Templates on page 50 Usersets on page 50 ki NOTE Problems that can be caused by exporting data using DTT from different versions of GCOS are described in Impacts Caused by Migrating from AGCC to GCOS on page 50 DAT Files CEL Files 48 Affymetrix Data Exchange Console 2 0 User s Guide Converting GCOS DAT files to Command Console format preserves the pixel intensity and both the global and subgrid coordinates The Command Console DAT format stores the global grid and subgrid pixel coordinates as floating point values to support sub pixel gridding GCOS DAT files save the global grid pixel coordinates as integral values and subgrid pixel coordinates as floating point values The GCOS DAT files stores the cell coordinates of each subgrid This information no longer exists in the Command Console DAT file The subgrid cell coordinates are instead read from the SMD file in Command Console The Command Console DAT file preserves most of the GCOS DAT header information but not all The following lists the GCOS DAT header data that has been removed or may be missing from the Command C
32. arch result chapter 1 Welcome to the Data Exchange Console 3 3 Continue to click Find Next to view each successive search result Screen Captures The steps outlining procedures are frequently supplemented with screen captures to further illustrate the instructions given The screen captures depicted in this manual may not exactly match the windows displayed on your screen Additional Comments El TIP Information presented in Tips provide helpful advice or shortcuts for completing a task NOTE The Note format presents important information pertaining to the text or procedure being outlined F IMPORTANT The Important format presents important information that may affect the accuracy of your results CAUTION Caution notes advise you that the consequence s of an action may be irreversible and or result in lost data a WARNING Warnings alert you to situations where physical harm to person or damage to hardware is possible Resources Online Documentation This manual is available in Adobe Acrobat format as pdf files in the download package for AGCC and is readable with the Adobe Acrobat Reader software available at no charge from Adobe at http www adobe com The content of this manual is available in context sensitive online help accessible by clicking the Help buttons in the Data Exchange Console 4 Affymetrix Data Exchange Console 2 0 User s Guide Technical Support Affymetrix provides technical
33. by file basis o Error condition File will not be exported Experiment Experiment name Type Type of data CEL DAT CHP GRD JPG Conflict Brief description of the conflict if any Resolution Automatic resolution to the conflict Error Description of a condition that cannot be resolved NOTE CHP files created with the new expression algorithms e g PLIER RMA iterPLIER and genotyping algorithms e g BRLMM P Birdseed cannot be loaded into GCOS and will not be included in the DTT file E Affymetrix Data Exchange Console Review the data before you export it from Command Console Review the following items and click Export to begin exporting the files To review all conflicts click Review Conflicts To see more detail for an experiment click the icon in the first column If there is an error with an experiment it cannot be exported Experiment DAT CEL CHP JPG BRD Conflict Resolution Error Batch j Batch2 Batch3 GCOS 1 3 GCOS 1_1 3 Rename GCOS 1 Figure 4 7 DTT export Review Data Conflicts arise because of discrepancies between the data in the different AGCC files being exported Click in a row to display the Detailed Validation Results for the experiment being exported Figure 4 8 chapter 4 DEC Export 43 ES Detailed Validation Results for Build37FU133a 1 TBR Data Name Data Type Error Build37EU133a 1 Experiment Build37EU133a_1 DAT DAT Data Build37EU133a_1 JPG JP
34. conflicts or conflicts resolved In progress 9 Error condition File will not be exported Experiment Name of exported experiment Message Particular file causing problem DAT template etc After the export is finished The DTT file is created e Click View Errors to view the error log or Click Start Again to export more files or Click Finish to close the DEC window The exported data is visible in the AGCC Data folder Chapter j EL i Ez E TT i _ i Te i Li ii E t LEM I 4 i E a Ta i si 1 g x i E m L i N it f _ Oi IMPACTS ON DATA There are differences in the way GCOS organizes and stores data and the way AGCC does These differences can cause impacts when you copy data from one to the other The impacts may vary depending upon The software source for the data being imported MAS 5 x and the different versions of GCOS The type of file being transferred DAT CEL and CHP The array type expression reseg mapping etc The type of algorithm used for processing the data e Which DEC process is used file to file or system to system These impacts are described briefly in this chapter of the DEC manual e Impacts Caused by Migrating from GCOS to AGCC on page 47 Impacts Caused by Migrating from AGCC to GCOS on page 50 Impacts Caused by Migrating from GCOS to AGCC The differences in file formats and data org
35. ded parent file information and associated with a Sample ARR file that will be created upon import You can select Sample and data files for import and move data files using drag and drop from one group to another to accommodate special circumstances If you are importing the following flat files Figure 3 23 Se C Test DataWEC_Test_Files FlatFilelmport File Edit View Favorites Tools Help LU FN F Back 9 E pi Search Folders sy J7 X ie EBk Address C Test DatalDEC_Test_Files FlatFileImport k Name Size Type Date Modified Exp with Template CEL 157 KB AGCC CEL File 4117 2008 1 25 PM Exp with Template CHP 6 KB CHP File 11 15 2006 3 52 PM 2 Exp with Template DAT 2 442 KB AGCC DAT File 4 17 2006 1 25 PM 21 objects My Computer Figure 3 23 Data files to be imported chapter 3 DEC Import 29 Y ou will see the following file group in the Select Files list Figure 3 24 E Ele Exp with Template ARR Sample File created during import mE Exp with Template Array Name assigned during import j 2 Exp with Template DAT DAT File M Exp with Template CEL cet File M Exp with Template CHP CHP File Figure 3 24 Sample file with Array name and data files 2 Select the checkbox es for the file s you with to import Selecting the checkbox for a parent file automatically selects all of the child file checkboxes you can deselect individual child checkboxes 1f desired Y ou can also make and
36. e 5 Starting the Data Exchange Console 0 0 0 0 ee 5 GCOS AGCC File Differences ES SS KIRI ee 6 File Format IMPACTS 4 vase N EE ara oe ak ark el aut he ae Bee we edr 9 Import Conflicts and EMOS aaa a a a a kala a alal cau a a alla al ala ati 9 slee ie AA OE EO EN OE eens AE HF Dn 10 Importing HT Array Plate Scanner Files SS SS SS SS SS SS eee 11 DEE DOEL ss a ke a e an d awne ASE G r ar xe ak d m le eee A e dnd 13 selecting Import Method kk SESSE ee 13 MOOG DT ARES e sa a Y n an SEE WW eee ene eee A 15 Importing From GCOS Connect kk YEKEK d af GEKEER N 22 Importing MAS GCOS Flat Files AYY KK KK KIRI K K IY 27 Importing HT Array Plate Scanner Data KIIR KII KII I KII 31 Bile RAAD OR NE ER a ae 37 Choosing How to Select Files for Export 00 37 Using the Filter RER ae kK kK KE ee KI KIRI O KI K K KIR K KI E 38 selecting Sample Files for Export ci 40 Selecting a Location kk kk KK ee 41 Reviewing Data and Fixing Conflicts 0 0 0 0 cee eee 42 Bee od s k a a xak dee i A tii eae e 2 QR h sk n dn EE eee ce J n amp d0 5 45 Impacts on Data ss RE kk kk kk kk a a RES RE kk kk ka a ak ka 47 Impacts Caused by Migrating from GCOS to AGCC 47 Impacts Caused by Migrating from AGCC to GCOS 50 ii Affymetrix Data Exchange Console 2 0 User s Guide Chapter gx
37. ect sample user sample date sample template name all sample template attribute names types and values with the following exceptions Integer is converted to floating point number Time attribute is converted to text In Command Console the sample data is saved in the Sample ARR file Experiment Data Converting GCOS experiment data to Command Console format preserves the following data experiment name array barcode probe array type assay type userset name automation flag experiment date all experiment template attribute names types and values with the following exceptions Integer is converted to floating point number Time attribute is converted to text This information is saved in the Physical Array element of the Sample file in Command Console Most of the GCOS scan information is written to the Command Console DAT header See the DAT file section for further details The GCOS hybridization information is preserved in the Command Console array audit log The log contains protocol name operator name date device name station ID station number module number number of stages each step in the protocol 50 Affymetrix Data Exchange Console 2 0 User s Guide Templates Converting GCOS templates to Command Console format removes the distinction between a sample and an experiment template and removes the notion of an active template The template name and attribute names types values con
38. en displays the following columns Status Icon Indicator of the status of the import No conflicts or conflicts resolved In progress 9 Unresolvable conflict error condition File will not be imported Plate Name Name of the plate Peg Imported Number of array peg with data imported number of total array pegs on array Message Particular file causing problem DAT template etc Click on the Details button to display the Detailed Plate Results window Figure 3 35 for the experiment being imported 36 Affymetrix Data Exchange Console 2 0 User s Guide ES Detailed Plate Results Samples REIS CHP Message 550001 4037283112808226 032008 HTHWS_V _V_inhouse_24 2 405 196 98 550001 4037283112808226_032008_HTHWS_V_V_inhouse_24 2 407 98 98 550001 4037283112808226_032008_HTHWS_V_V_inhouse_24 2 409 98 98 550001 4037283112808226_032008_HTHWS_V_V_inhouse_24 2 B05 98 98 550001 4037283112808226_032008_HTHWS_V_Vinhouse_24 2 B07 98 98 550001 4037283112808226_032008_HTHWS_V_V_inhouse_24 2 B09 98 98 550001 4037283112808226_032008_HTHWS_V_Vinhouse_24 2 005 98 98 550001 4037283112808226_032008_HTHWS_V_Vinhouse_24 2 C07 98 98 550001 40372831 12808226 032008 HTHWS_V_V_inhouse_24_2 C09 98 98 550001 4037283112808226_032008_HTHWS_V_V_inhouse_24 2 D05 98 98 550001 40372831 12808226 032008 HTHWS VV inhouse 24 2DO7 98 98 550001 40372831 12808226 032008 HTHWS VV inhouse 24 2DOS 98 98 550001 4037283112808226_032008 HTHWS VV inhouse 24 2E0
39. f you wish to exclude the DAT data from the import 3 Click Next The Select Location window opens see below Selecting a Location The Select Location window Figure 3 6 allows you to select a location to place the imported data E Affymetrix Data Exchange Console Where would you like to save the imported data Select Save Location Type the folder path or browse to the folder where you wish to save the data EEk Save to C Command_Console New_Root Browse Estimated Disk Space Required 919 MB Space Available 11301 MB Create Project Subfolders Check the box if vou wish to create project subfolders within the selected folder to maintain GCOS project relationships Create Project Subfolders Figure 3 6 DTT Import Select Save Location 17 18 Affymetrix Data Exchange Console 2 0 User s Guide 1 Select the location by typing the path into the Location box using path completion or A Click the Browse button The Browse for Folder window opens Figure 3 7 Browse For Folder My Documents My Computer ee Local Disk C KC archive 5 Archive_calvin_Docs_03_16 KC cache KO Calvin Configurations CC Calvin_Docs O Calvin W amp AD Command_Console v amp Figure 3 7 Browse for Folder window B Browse to the folder with the files to be imported C Click OK 2 Select Create Project Subfolders if you wish to create project subfolders
40. ffymetrix Data Exchange Console 2 0 User s Guide Browse For Folder Desktop Er My Documents Ev My Computer E a My Network Places Recycle Bin E 7_06 O Affymetrix_Downloads E O CNAT 401 B FlatFileImport 2 GCOS_Tech_Notes_Hauw O Library D New Folder Ji Figure 3 28 Browse for Folder window B Browse to the folder with the files to be imported C Click OK 2 Enter the location of the AGCC Library Folder by typing the path into the Location box or using the Browse Button 3 Enter the destination location for the imported files in the Save Data To box by typing the path into the box or using the Browse button 4 Click Find Files to Import The window displays a list of files to be imported in the Step 2 Review list of files to be imported list E Affymetrix Data Exchange Console HT Array Plate Scanner Directories searching completed Step 1 Select source and destination data folders DAT Folder AGCC Library Folder Y DecHtData completePlates plate dat C Command_Console Library CEL Folder Save Data to DecHtD ata completePlatesplatel cel C Command_Console Data HT_Import CHP Folder C Same as CEL Folder Y DecHtData completePlates plate chp Find files to import Step 2 Review list of files to be imported Import Details Plate Name Message 5500014035098021908485 PZ_0311 24 24 24724 Estimated Disk Space Required 63
41. file s with the GCOS project and sample information The DAT CEL CHP data will be transferred into AGCC under the appropriate project sample and the data files will be converted to the appropriate AGCC format e GCOS Connect Direct connection between GCOS and AGCC You can use this to transfer data directly from a GCOS Server into AGCC or from a GCOS Client installation on the same computer as the AGCC installation The DAT CEL CHP data will be transferred into AGCC under the appropriate project sample and the data files will be converted to the appropriate AGCC format IMPORTANT If you wish to connect to a GCOS server with DEC you must install DEC for GCOS Server on the GCOS server If DEC for GCOS Server is not installed on the server you will see a permission error when you try to connect See Installing DEC for GCOS Server on the GCOS Server on page 19 of the AGCC 2 0 Installation Instructions for more information e MAS 5 x GCOS 1 x Data Select this option to transfer in DAT CEL CHP data that do not have the XML file with the GCOS project and sample information Other information required for transfer IN will be regenerated using the information available in the DAT CEL headers The data is copied to the user provided folder HT Array Plate Scanner HTAPS Data Select this option to transfer in DAT CEL CHP data for an array plate Other information required for transfer IN will be regenerated using the information available in the D
42. iles you would like to import O User COI Assay Type Probe Array Type HG U133A Project CO Sample Filter Date Experiment Date Range O DAT Date Range m to r v Figure 3 16 Filter Data To filter experiments 1 Select the GCOS attribute types and attributes from the following items User User who created the sample in GCOS Assay Type General type of array e Mapping e Expression Universal Resequencing Probe Array Type of probe array analyzed Type Project Project that the probe array was listed under Sample Sample Name used for the probe array A Click the checkbox next to the attribute name B Select an attribute from the drop down list 2 Filter by dates by doing the following A Select an option from Experiment Date Dates when the experiment was created Range DAT Date Range Dates when the array was scanned chapter 3 DEC Import 25 B Select a date or range of dates for file creation 1 Select the From checkbox 2 Click the arrow at the date displays the current date A calendar for the current month appears Figure 3 17 Filter Date Experiment Date Range O DAT Date Range 3 20 2007 to L 3 20 2007 M March 2007 Tue Wed Thu 27 28 1 Sun Mon 25 26 4 5 6 7 6 9 10 11 12 13 14 15 16 17 18 19 I 21 22 23 od 25 26 2 28 29 30 3l 1 2 d 4 5 6 _ Today 3 20 2007 Figure 3 17 From Calendar 3 Select a date for the s
43. imated Disk Space Required 6309 MB Space Available 46954 ME Figure 3 31 Error message for duplicate files If these error messages appear you will need to go to the folder with the files you wish to import and resolve the problem there before importing The resolution may involve e Finding missing files Moving duplicate files 34 Affymetrix Data Exchange Console 2 0 User s Guide Y ou can view a detailed list of the files for individual arrays in the Detail Plate Results list e Click the Details button in the Review List Figure 3 32 Step 2 Review list of files to be imported Import Details Plate Name DAT Message CEL CHP 5500014037283112808226_032006 Duplicated Bupisate zd Duplicate Details button Figure 3 32 Detailed button in the Results List The Detailed Plate Results dialog box Figure 3 33 opens H Detailed Plate Results Samples mini DAT CEL CHP Message 550001 4037283112808226 032008 HTHWS V V inhouse 24 2 405 196 98 550001 40372831 12808226_032008_HTHWS_V_V_inhouse_24_2 407 98 98 550001 40372831 12808226 032008 HTHWS VV inhouse 24 2A09 98 98 550001 40372831 12808226_032008_HTHWS_V__inhouse_24_2 B05 98 98 550001 40372831 12808226_032008_HTHWS_V_V_inhouse_24_2 B07 98 98 5EO0D14037283112808226 032008 HTHWS VV inhouse 24 2BOS 98 98 550001 40372831 12808226_032008_HTHWS_V_V_inhouse_24_2 C05 98 98 550001 40372831 12808226_032008_HTHWS_V_V_inhouse_24_2 CO7 98 98 550001 40372831 12808226
44. imported into AGCC e Duplicate attribute names in a template e Discrepancies in the Data Types and control values for attributes in AGCC templates and templates to be imported Sample and experiment templates with the same template name Usersets Userset conflicts occur when the imported userset has the same name as a userset already in Command Console but with different values or probe array types Physical Array Name Conflicts Physical array name conflicts between imported data set and physical arrays already in AGCC are not considered Unresolvable Conflicts Notices Typical unresolvable conflicts involve A barcode is used by a sample file already in AGCC Export Conflicts Certain conflicts can arise when migrating data from AGCC to GCOS Sample File User Attribute Names Due to namespaces in user attributes samples in AGCC can have multiple attributes with the same name GCOS can not handle this situation so these attributes need to be renamed for export to GCOS chapter 2 Introduction to Data Migration 11 Data File or Experiment Name conflicts Within the data being exported since AGCC can have many Sample and Data files with the same name but in different folders there can be name conflicts when exporting data into a DTT file Exported DAT and CEL Names Mismatch DTT expects that a CEL file that is based on a DAT file will have the same root name as the DAT file If the CEL file does not then DTT will fai
45. ing an override option and typing the override text Override Action TEEL N ETE Gens 1 3 senlliz z wilh adieren expelment of the same nameand has been Tenamed GCOS 1 1 2 GCOS_1 3 4 Experiment Therm Conflict Description Override Save Cancel Figure 4 10 Review Conflicts The window displays a list of conflicts with the following information Status Icon Indicator of the status of the export No conflicts or conflicts resolved AP Unresolvable conflict files will be exported on a file by file basis 9 Unresolvable conflict error condition File will not be exported Experiment Name of exported experiment Items Particular file causing problem DAT template etc Conflict Description of the problem Description Override Resolution automatically selected Action Override Enter a new name for the file to override the automatically created name 4 Enter new file names as desired 5 Click Save to close the Review Conflicts window and enter the new file names 6 Click View Errors to review files that cannot be exported at all The View Errors window opens Figure 4 11 chapter 4 DEC Export 45 Fen View Errors Experiment Data Name Data Type Close Figure 4 11 View Errors The window displays a list of files and data with the following information Experiment Name of exported experiment Data Name Particular file causing problem DAT template etc Data Type Type of
46. l to import it To get around this limitation DEC will rename the DAT file to match the child CEL file and show a conflict resolution The user may change the root name of the DAT and CEL file A consequence of this limitation is that only one CEL file per DAT file may be successfully exported Different Samples With the Same Name In AGCC many samples can have the same name and have different attributes or belong to different projects DEC will assume that every sample file is distinct regardless of the name When two samples with the same name are added to the same DTT file DEC shall rename the samples and allow the user to change the name through the conflict resolution dialog Importing HT Array Plate Scanner Files HT array plates can be processed in GCOS For each array on a plate GCOS produces 84 or 98 mini DAT files e 1 CEL file 1CHP file When the GCOS HT Array Plate data is imported into AGCC using DEC the following AGCC files for each array are created e DAT file e 1 CEL file e 1 CHP file The mini DATs get consolidated during import and the CEL and CHP files get imported in the AGCC format See Chapter 8 Using the AGCC Viewer in the AGCC 2 0 User s Guide for more information about how HT Array Plates Scanner files are set up 12 Affymetrix Data Exchange Console 2 0 User s Guide an 9 i ai ku Chapter DEC IMPORT ER fa ar MUM aha IE lI You can import GCOS data i
47. nto AGCC using several different methods For any import workflow you follow the same set of steps Select the import option you wish to use Select the file s to be imported Select experiments from the file optional Select or create a project for the imported files Check for conflicts Resolve conflicts if necessary li N RR n Import data Selecting Import Method Y ou can import data using the following methods Figure 3 1 Importing DTT 1 1 Archive or Flat Files see page 15 Using GCOS Connect see page 22 e Importing MAS 5 x GCOS 1 x Flat Files see page 27 Importing HT Array Flat Files see page 31 14 Affymetrix Data Exchange Console 2 0 User s Guide Be Affymetrix Data Exchange Console How would you like to import data into Command Console The method used will depend upon The type of system The file type used to store data The availability of a connection between the GCOS Server or Client and the computer running AGCC Import Optian DTT 11xFiles In Archive or Flat File format GCOS Connect for connection with GCOS systems O MAS 5x GCOS 1x Files in flat file format HT Array Plate Scanner HTAPS Data Figure 3 1 Select Import Method e DTT 1 1 x Files In Archive or Flat File format Select this option to transfer in data from DTT Archive files or as a set of flat files with associated XML files The flat files or DIT Archive file must have the associated XML
48. on page 17 Reviewing Data See Reviewing Data on page 18 Tracking Import Status See Tracking Import Status on page 21 chapter 3 DEC Import 31 Importing HT Array Plate Scanner Data HT Array Plate Scanner HTAPS data can be imported into AGCC 2 0 for management and use Experiment information is not imported HT Array Plate Scanner The HT Array Plate Scanner window Figure 3 27 allows you to select a set of data for one or more array plates to import NOTE We recommend moving all the peg level data miniDAT CEL and CHP files together Reconnector does not support re establishing relationships between HT data files if they are imported separately into AGCC E Affymetrix Data Exchange Console HT Array Plate Scanner Step 1 Select source and destination data folders DAT Folder AGCC Library Folder C Command_Console Librarp CEL Folder Save Data to Browse Browse CHP Folder C Same as CEL Folder Find files to import Step 2 Review list of files to be imported Import Details Plate Name CHP Message Estimated Disk Space Required 0 MB Space Available 0 MB Figure 3 27 HT Array Plate Scanner window To import GCOS HT array plate data 1 Select the location of e DAT files e CEL files e CHP Files Type the path into the appropriate box using path completion or A Click the Browse button The Browse for Folder window opens Figure 3 21 32 A
49. onsole DAT header GCOS Data Removed from AGCC files e Scan Power Scan Temp e Scan Speed Mean of the pixel intensities Standard deviation of the pixel intensities Average Offset Offset Stddev e Offset samples e Scan Comments Scan Operator e Verify Grid e Grid algorithm parameters e Grid algorithm name e Number of scans e Any GCOS DAT data that is missing and is present in the GCOS system The barcode has been added to the Command Console DAT file header Converting GCOS CEL files to Command Console format preserves the CEL intensity error stdev number of pixels and the mask and outlier flags The Command Console CEL file preserves most of the GCOS CEL header information including the global grid coordinates from the DAT file the cell rows and cell columns the probe array type and the algorithm parameters The following table lists other header information that is not preserved in Command Console OffsetX OffsetY Axis invertX Axis invertY e swap Y Algorithm parameters not in GCOS CEL e CEL Algorithm name GHP Files chapter 5 Impacts on Data 49 CHP files created with the new expression algorithms e g PLIER RMA iterPLIER and genotyping algorithms e g BRLMM_P Birdseed cannot be loaded into GCOS and will not be included in the DTT file Sample Data Converting GCOS sample data to Command Console format preserves the following data sample name sample type sample proj
50. s and Errors on page 9 These types of inconsistencies can also cause conflicts when transferring data from AGCC to GCOS For more information see Export Conflicts on page 10 Importing HT Array Plate Scanner data involves some special issues See Importing HT Array Plate Scanner Files on page 11 for more information Starting the Data Exchange Console To start the Data Exchange Console e Click the Microsoft Windows Start button 2 start and select Programs Affymetrix Data Exchange Console The Welcome window opens Figure 2 1 The Welcome window opens when vou first start DEC This is where you can choose e Import Data e Export Data 6 Affymetrix Data Exchange Console 2 0 User s Guide ES Affymetrix Data Exchange Console Welcome to the Affymetrix Data Exchange Console Would you like to move data into or out of Affymetrix GeneChip Command Console The Data Exchange Console Wizard helps move data between leqacy Affymetrix systems and Affymetrix GeneChip Command Console Throughout this process you can select the data to be moved how itis moved the location of the new file or files Note It may take a significant amount of time to transfer large amounts of data Select Data Transfer Option Import Data Into Command Console from GCOS Export Data Out of Command Console to a DTT File License Figure 2 1 Welcome window Use the buttons at the bottom to Help Open the Online help
51. se the DEC window The imported data is visible in the AGCC Data folder Importing From GCOS Connect GCOS Connect allows you to transfer data from a GCOS system on another computer or on the computer with AGCC in one step You will not have to export the files from GCOS using DTT ki NOTE DTT must be installed on the GCOS system you are importing files from to use GCOS Connect Selecting a GCOS System The Select GCOS System window Figure 3 14 allows you to select a GCOS system from which to import data IMPORTANT If you wish to connect to a GCOS server with DEC you must install DEC for GCOS Server on the GCOS server If DEC for GCOS Server is not installed on the server you will see a permission error when you try to connect See Installing DEC for GCOS Server on the GCOS Server on page 19 of the AGCC 1 1 Installation Instructions for more information chapter 3 DEC Import 23 ES Affymetrix Data Exchange Console What GCOS system would you like to connect to GCOS Connect allows you to import data directly from a GCOS system Select GCOS System Type the system name or browse to the system or select this system using the check box Connect To STGo1 CI This system Choose Import Option Exclude previously migrated experiments Find use filters to find experiments and types of data to import O Browse choose specific experiments and types of data to import Figure 3 14 Select GCOS System
52. sible impacts before transferring data You can learn more about file format impacts in Chapter 5 Impacts on Data on page 47 Import Conflicts and Errors Import conflicts occur when there is a discrepancy or duplication in the data to be imported The discrepancy can be between the data to be imported and the data in AGCC already or between two files in the set of data to be imported These conflicts can be detected by DEC and resolved by correcting the discrepancy or renaming the item to be imported that is causing the discrepancy 10 Affymetrix Data Exchange Console 2 0 User s Guide These discrepancies can involve e File Names below e Sample and Experiment Template Names on page 10 e Usersets on page 10 e Physical Array Name Conflicts on page 10 e Unresolvable Conflicts Notices on page 10 For more information about resolving conflicts see the relevant sections of Chapter 3 DEC Import on page 13 An etror is a conflict or other problem that cannot be resolved File Names A file name conflict arises when You are trying to import a file with the same name as a file that is already in AGCC You are trying to import two different files with the same name Sample and Experiment Template Names Template conflicts can be caused by e Discrepancies in the attributes in the template used in AGCC and the attributes in the templates used for the data being imported e Discrepancies between two different templates being
53. support to all licensed users via phone or E mail To contact Affymetrix Technical Support Affymetrix Inc 34200 Central Expressway Santa Clara CA 95051 USA E mail support affymetrix com Tel 1 888 362 2447 1 888 DNA CHIP Fax 1 408 731 5441 Affymetrix UK Ltd Voyager Mercury Park Wycombe Lane Wooburn Green High Wycombe HP10 OHH United Kingdom UK and Others Tel 44 0 1628 552550 France Tel 0800919505 Germany Tel 01803001334 E mail supporteurope affymetrix com Tel 44 0 1628 552550 Fax 44 0 1628 552585 Affymetrix Japan K K Mita NN Bldg 16 Floor 4 1 23 Shiba Minato ku Tokyo 108 0014 Japan Tel 81 03 5730 8222 Fax 81 03 5730 8201 www affymetrix com Chapter BERR aa i jili Bi i SEN f i gt INTRODUCTION TO DATA MIGRATION The Data Exchange Console DEC for AGCC and the Data Transfer Tool DTT for GCOS allow you to migrate data From GCOS to AGCC From AGCC to GCOS GCOS and AGCC use different systems to organize the data and different formats for the data files themselves These differences are a potential source of problems when you migrate data and can have impacts on the data For more information see GCOS AGCC File Differences on page 6 File Format Impacts on page 9 In addition inconsistencies in the data or duplicated names in GCOS and AGCC can cause conflicts during data import For more information see Import Conflict
54. t be transferred because the associated experiment LsersetMaskA cannot be transferred UsersetMask4_dup_AbsMaskScaling CHP Data Data file UsersetMaskA_dup_AbsMaskScaling CHP cannot be transferred because the associated experiment UsersetMaskA4 cannot be transferred Close Figure 3 9 Detailed Validation Results The list displays the following information about the experiment Data Name Name of file Data Type Type of file being imported or created Error Brief description of the condition that cannot be resolved if any To review the data for import 1 Review the list for conflicts Conflicts will automatically be resolved but you can override the automatic resolution using the Review Conflicts window 2 Click the Review Conflicts button The Review Conflicts window opens Figure 3 10 20 Affymetrix Data Exchange Console 2 0 User s Guide ES Review Conflicts We have found the following conflicts You may change the resolution by selecting an override option and typing the override text Experiment Item Conflict Description Override Action Override AP Build37EU133a Build37EU133a Barcode is already used in Command Console 51068100247207011104300004891 140 g GCOS 1 3 GCOS 1 3 Barcode is already used in Command Console 5106810024720701 1104300004891 236 Grcos 1 3 DTT 1 3 Userset P ARAMS Parameter file DTT 1 3 Userset PARAMS already exists in Command Console Rename userset Yo
55. t by To select experiments 1 Select the checkbox es for the experiment s you with to import Y ou can also make and clear selections using the Select All and Unselect All buttons a NOTE Files to which you do not have permission to access on GCOS are displayed in this list An error message will be displayed when you go to the Review page Y ou can also make and clear selections using the Select All and Unselect All buttons 2 Deselect Include DAT data if you wish to exclude the DAT data from the import 3 Click Next The Select Location window opens Selecting a Location See Selecting a Location on page 17 Reviewing Data If you are trying to import files that you do not have access to in the GCOS Server you will see the following error message Figure 3 19 Access was denied to the Following experiments scan autoe Figure 3 19 Access denied message Y ou will need to contact the administrator for the GCOS Server to get access to the files See Reviewing Data on page 18 for information about checking for data conflicts and errors chapter 3 DEC Import 27 Importing Data See Tracking Import Status on page 21 Importing MAS GCOS Flat Files You may wish to import MAS and GCOS flat files from earlier versions of GCOS These files will not have the sample information that is available with DTT files or GCOS Connect When you are importing the DAT CEL and CHP files by themselves DEC will create a S
56. tart of the range You can move from month to month by clicking the lt and gt buttons If you only select a start date the filter will display only the files created on or after that date To select a range of dates e Select a date for the end of the range If you only select an end date the filter will display only the files created on or before that date 3 Click Next The Select Experiments window appears Selecting the Experiments The Select Experiments window Figure 3 18 allow you to select individual experiments in the GCOS system E Affymetrix Data Exchange Console What experiments would you like to import Select Experiments Select the experiments you wish to import Experiment User Date Assay Probe Array Type Type RI auto c thoang 5 24 2007 Expression HG U133A Scan thoang 5 23 2007 Expression HG U133A Select All Unselect All Import DAT data If you wish to exclude DAT data uncheck the box below Include DAT data Figure 3 18 GCOS Connect Import Select Experiments 26 Affymetrix Data Exchange Console 2 0 User s Guide The list displays the following information Experiment Experiment name User User who created the sample in GCOS Date Date of file creation Assay Type General type of array Mapping Expression Universal e Resequencing Probe Array Type Type of probe array analyzed You can sort the list order by clicking in the header of the column you wish to sor
57. trolled value lists and required flags are preserved in template files The imported template files are available for the user in Command Console Usersets Converting GCOS usersets to Command Console results in one or more PARAM files per userset one for each probe array type defined in the userset The format of the PARAM file name includes the userset name and probe array type The name type and value of each parameter is preserved Impacts Caused by Migrating from AGCC to GCOS You can export data from AGCC in DTT format and import it into different versions of GCOS There are some issues that arise when you do that described in this section The AGCC data is exported into DTT files using GCOS 1 4 formats When the DTT file is imported into GCOS it will be converted to earlier GCOS formats GCOS 1 x if necessary The GCOS versions are backward compatible but not forward compatible That is you can view a GCOS 1 1 file in GCOS 1 4 but you may not be able to use a GCOS 1 4 file in GCOS 1 1 GCOS File Format Changes The file formats used in different versions of GCOS have changed to accommodate new features and to improve performance These file format changes may cause data impacts when importing or export data from GCOS and AGCC The file formats that may change are summarized in the table below Table 5 1 Software versions and data file versions MAS 5 x GCOS 1 0 1 1 x GCOS 1 2 GCOS 1 3 GCOS 1 4 DAT File DAT v1 DAT v1
58. uter EE 12 14 2006_104220_AGCC DTT My Recent a My Network Places D Calvin Docs Documents 77 06 BO Calvin W6G 4ffymetrix_Downloads B3 CC_Data EQ CNAT_401 mcc Software FlatFileImport E DTT 1 3 Expression DTT E GCOS_Tech_Notes_Hauw E DTT 1 4 Expression DTT Library BH drive ORC Revs pe Shortcut to Local Disk C O Quick Start Template BO Shortcut to rallso Rich Allsop E3 UI_Suggestior simulators Pr Test Files K wkgrp addendum My Computer My Documents File name 3202007 034400 AGCC DTT 5S l My Network Save as type DTT Files DTT Figure 4 6 Browse select project file B Browse through the directory to select a location for the DTT file Enter a new name for the DTT file in the File Name box or use the default name C In the Save As window click OK Space required and available is displayed 2 Select Create Multiple Files if you wish to split the data into smaller files 3 Select a file size from the drop down box 42 Affymetrix Data Exchange Console 2 0 User s Guide 4 Add comments in the Comments box if desired 5 Click Next The Review Data window opens Reviewing Data and Fixing Conflicts The Review Data window Figure 4 7 displays a list of the files to be exported with the following information Status Icon Indicator of the status of the export No conflicts or conflicts resolved AP Unresolvable conflict files will be exported on a file

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