Hi Henrik Here are the links:
1) http://groups.google.com/group/aroma-affymetrix/web/total-copy-number-analysis-6-0 Under "Identification of copy-number regions" cbs <- CbsModel(ces1, ces2) 2) In windows, under C:\Program Files\R\R-2.9.1\library \aroma.affymetrix\testScripts\system\chipTypes\GenomeWideSNP_6, R script file by name "test20080729,6.0,CN,refSet.R" # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Segmentation with specific reference set # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Use the robust average of the first three arrays as a reference cesR <- extract(cesN, 1:3); ceR <- getAverageFile(cesR); print(ceR); sm <- CbsModel(cesN, ceR); ===================== So in my context, i translated that as given below: Analysis is done on two paired samples (normal1: tumor1). Script 1 (Link 1) ========================= # Use the robust average of the first array as a reference cesR <- extract(cesN, 1); cesL <- extract(cesN, 2); sm<-CbsModel(cesR,cesL) ========================= Script 2 (from the link 2: modified example script) # Use the robust average of the first array as a reference cesR <- extract(cesN, 1); cesL <- extract(cesN, 2); ceR <- getAverageFile(cesR); sm <- CbsModel(cesN, ceR); ========================= First question would be: did I cross stitch two different methods (analyses) and came up with a hybrid script :(? If not, second one would be , what is the difference ? Regards suresh --~--~---------~--~----~------------~-------~--~----~ When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
