Hi Michelle, I've just added vignette 'Paired parent-specific copy-number segmentation (Paired PSCBS) (low-level API after AS-CRMAv2)':
http://aroma-project.org/vignettes/PairedPSCBS-lowlevel See if that helps /Henrik On Fri, Nov 11, 2011 at 1:02 PM, Michelle <suyi...@gmail.com> wrote: > Dear aroma community, > > We are trying to do paired CBS analysis on some Affy SNP 6.0 data > using the R package "PSCBS", but not sure how to extract the total CN > and BAF values from the raw array files (.CEL) into the needed format > (pasted below). It seems aroma.affymetrix has some relevant functions > but there are few examples to follow. Could someone provide some > sample code on this? Thanks! > > > chromosome position CT betaT CN > betaN > SNP_A-8575125 1 554484 1.8778996 0.06460427 1.8856720 > 0.1161352 > SNP_A-8575115 1 554636 0.1659543 0.64621653 0.2282602 > 0.6919347 > SNP_A-8575371 1 557616 2.1193934 0.82567971 2.3405546 > 0.8425635 > SNP_A-8709646 1 711153 1.3974123 0.25975011 2.2465997 > 0.1765471 > > CT: total tumor copy number > betaT: tumor allele B fractions (BAFs) > CN: total matched normal copy number > betaN: matched normal BAFs > > -- > 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/ > -- 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/
