Hi, It took me some time (and finding a colaborator to help me) to write an R package wrapping my copy number algorithm GADA since I have been busy with so many other things.
I used the answer you kindly provided some time ago to add my algorithm in aroma.affymetrix: http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/614c7cdc1cbb8cf5/655efedf35aa6a3c?lnk=gst&q=theta+copy+number#655efedf35aa6a3c I think it was very detailed and I figured out the gaps by looking how the CBS and GLAD cases were handled. I really appreciate it. I think we still have to do some more checks to make sure everything is working well. So far, I'm quite happy that it looks like it goes much faster than CBS method. While implementing, I noticed that when I extract the copy number intensities, you also estimate something that looks like the standard deviation sdM... > data <- getRawCnData(gada, ceList=ceList, refList=refList, chromosome=22, > verbose=-10); > str(data) num [1:74, 1:6] 15685581 16604328 16958128 17506879 18008688 ... - attr(*, "dimnames")=List of 2 ..$ : NULL ..$ : chr [1:6] "x" "M" "sdTheta" "sdM" ... Is this correct? If that is the case I would be interested in knowing how are these SD calculated... I may be able to use them in my algorithm. Finally, one last question is that I get a few probes with the M value NA. I guess it is fine, but I just wonder how they arise. I really appreciate your help, Roger, --~--~---------~--~----~------------~-------~--~----~ 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 [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
