Yes, you can use the CRMA v2 methods instead of the CRMA v1 method for these older chip types as well. The only difference is that CRMA v2 was optimized (=optimized signal-to-noise ratios) only for GenomeWideSNP_5 and forward, but all practical purposes you can use CRMA v2 for your needs. I do this myself. So, yes, run doCRMAv2().
/Henrik On Tue, Jun 9, 2015 at 9:20 AM, Arshi Arora <arshiaur...@gmail.com> wrote: > > 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. -- -- 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.
