Hi Henrik, I have paired normal tumor files from chip type Mapping250K_Nsp I am following two vignettes - http://www.aroma-project.org/vignettes/PairedPSCBS-lowlevel/ *Vignette: Paired parent-specific copy-number segmentation* and
http://www.aroma-project.org/vignettes/CRMAv1/ *Total copy number analysis using CRMA v1 (10K, 100K, 500K)* I want to get the copy number of each SNP, so I want - ## NA06985 NA06991 NA06993 NA06994 NA07000 NA07019## SNP_A-1938296 -0.0402 0.0391 -0.0518 -0.0414 0.1967 0.0476## SNP_A-4259059 0.1519 -0.1174 0.2330 -0.1432 -0.2650 0.1086## SNP_A-1939610 -0.4355 -0.3506 -0.0181 0.0179 0.3192 0.2245 http://www.aroma-project.org/vignettes/calculating_raw_total_copy_numbers_manually/ h *Calculating raw total copy numbers manually. *This vignette tells us to follow vignette *- **Total copy number analysis using CRMA v1 (10K, 100K, 500K). *In this vignette I am doing the normalizing steps individually. My question is - Instead of doing correction of allelic crosstalk, quantile normalization, and fragment normalization can I just do doCRMAv2 for each pair and get its CnChipSizeEffect and then go to the vignette of calculating raw total copy numbers manually? I also want the BAF of these samples and I feel as if I am basically repeating normalizing step in order to get these 2 tasks. I have some 150 arrays. Thanks, Arshi -- -- 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 with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
