Preprocessing and analysis of Affymetrix micro.DOCVIP

Preprocessing and analysis of Affymetrix microarray data for library pooled shRNAs Dchip preprocessing of Affymetrix microarrays: 1. Create a folder containing cel files (eg GreatExpt_cel_files) 2. Create a folder to hold dcp (dchip) files (eg GreatExpt _analysis_yyddmm) 3. Open dchip (dchip2006_f5_070502.exe) 4. Under Analysis, select “Open group” 5. Name a new group if starting a new data set 6. Under Data source, click on Data directory, browse to the folder containing the cel files. 7. Make sure the CEL is selected if cel files are analyzed 8. Click on Options button near the bottom (Options can be selected and changed at any time) 9. Click on Analysis option (at the top) 10. Click on Working directory to locate folder created in step 2 above (GreatExpt _analysis_yyddmm) 11. Select Log2 transform expression values 12. Select DCP files in the working directory Deselect Check CEL file time tag Deselect Load probe data in memory Deselect Array has only PM probes 13. Select Consider measurement error when averaging 14. Select Omit Affymetrix control probe set at filtering and comparison 15. Click Model option (at the top) 16. For Model method, start with Average 17. For Background subtraction, start with using 5th percentile of region (PM-only) 18. Select Check single, array and probe outliers 19. For Probe sensitivity index (PSI) file, Choose Do not use for Usage 20. Under Normalization, choose Invariant set for Probe selection method; keep None for Probe set file; choose Running median for Smoothing method 21. Click OK to finish Options selections 22. Click on Other information (at the top) 23. Under CDF file, click the button after Select. Locate the CDF file (TRCBCx520397F.cdf) This is specific for the array you use 24. For Array type, select Barcode (last option) 25. Click OK to start preprocessing Dchip log file will show something similar to depending on your file