User`s Manual - BioDiscovery
Contents
1. Type Agilent FE sample Name File Filez Factor Gender Factor Tumor Type sample 1 C BrainTumorProjectiarray1 txt C BrainTumorProjectiarray1R txt M GBM sample C BrainTumorProjectiarray2 txt C BrainTumorProjectiarray2R txt F ADA sample 3 C BrainTumorProjectiarrays_tet C BrainTumorProjectiarray3R txt M ADA Please refer to the document specific for your data type for further information on how to load and process your data you will have to use the sample descriptor method to load replicate data Please note that when editing files in Excel starting a cell with an operator e g minus sign causes Excel to add and equal sign to the beginning of the cell Nexus will be unable to load this file So after creating the descriptor file open it in Notepad or similar software and remove the equal sign if present before loading the descriptor into Nexus 2012 BioDiscovery Inc support biodiscovery com 310 414 81002. DIO DISCOVERY INC NEXUS COPY NUMBER HOW TO PROCESS RAW DATA TO PROCESS REPLICATE DATA If you have more than one array for a particular sample technical replicates you can load these by adding additional File columns to the sample descriptor For dye swap experiments see further below The column header must be File suffixed with a number e g File1 File2 File3 etc File without a numerical suffix can also be used for one of the columns File Filel File2 File3 File4 Sample descriptor for Agilent samples with technical replicates Data Type Agilent FE sample Name File File Files Factor Gender sample 1 C BrainTumorProjectiarray1 txt C BrainTumorProjectiarray 11 txt C BrainTumorProjectiarray3 1 txt Ml sample 2 C BrainTumorProjectiarray2 txt C BrainTumorProjectiarray12_txt F sample 3 C BrainTumorProjectiarray3 txt 6C BrainTumorProject array13_txt Ml How the technical replicates are handled is determined by what settings are used for processing that data type within Nexus Combine Replicates Between Arrays is a parameter that can be modified via the Settings window Combine Replicates Between Arrays Mone ha Mean Median Analy Hone Type In the Chromosome view in the sample drill down probes from each array will be displayed in a different color The sample drill down shows the data prior to replicate combination operation so even if replicates between arrays were set to be combined during pr
3. ocessing the sample drill down will display the probes from each array for the sample The probe color for each array depends on the column header File blue File1 red File2 green File3 cyan File4 magenta FileS pink File6 orange All others gray Please refer to the document specific for your data type for further information on how to load and process your data 2012 BioDiscovery Inc support biodiscovery com 310 414 8100 BIODISCOVERY INC NEXUS COPY NUMBER HOW TO PROCESS RAW DATA DYE SWAP DATA With dye swap experiments for two color arrays two arrays are run for each sample where the dye used for the experimental and control samples is reversed on one array with respect to the other array Additional File columns are added to the sample descriptor as described above For analysis of dye swap data the intensity ratio needs to be reversed for one of the arrays and Nexus needs to know which one to reverse Ratio reversal is indicated by prefixing a minus sign to the column header Filel File2 Data for the two arrays is combined to remove dye effects and then the aberrations are displayed Any number of dye swap data can be added to each sample by adding additional columns and prefixing the column header with a minus sign for the array that needs to have its ratio reversed In the example below File and File2 refer to a pair of dye swap experiments for the samples in the project Data
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