Hi, Henrik, I have some Affymetrix SNP6 data on a resistant cell line model after compound treatment. I want to do a paired analysis comparing the resistant cell line data to the parental. To make sure that the changes I see in the paired analysis is indeed acquired aberrations, not simply a magnitude change between the resistant and parental, I also want to analyze the resistant and parental data separately against a common reference (e.g. Hapmap). So my question is how I can combine both a paired and an unpaired analysis in aroma affymetrix/cn.
Some codes I have for the paired analysis are as follows: library("aroma.affymetrix"); verbose <- Arguments$getVerbose(-8, timestamp=TRUE); options(digits=4); dataSet = "Resistant_model"; chipType = "GenomeWideSNP_6"; cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full"); dsC = doCRMAv2(dataSet, cdf=cdf, verbose=verbose); print(dsC); # paired analysis idxP <- match("Parental", getNames(dsC)); dsP <- extract(dsC, idxP); idxR <- match("Resistant", getNames(dsC)); dsR <- extract(dsC, idxR); cns2 <- CbsModel(dsR,dsP); print(cns2); ce2 <- ChromosomeExplorer(cns2); print(ce2); process(ce2, verbose=verbose); I have also loaded a set of preprocessed Hapmap samples as follows: ds <- AromaUnitTotalCnBinarySet$byName("SNP6_HAPMAP_FEMALE", tags="ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY", chipType="GenomeWideSNP_6"); print(ds); dsRef <- getAverageFile(ds, verbose=verbose); print(dsRef); I was wondering whether there is a way that will allow me to construct a AromaUnitTotalCnBinarySet consisting of: 1) Resistant, 2) Resistant and 3) Parental; then compare it to another reference set consisting of: 1) Parental, 2) Hapmap and 3) Hapmap. I understand that I can do the paired and unpaired analysis separately, but I want to generate one ChromsomeExplorer report consisting both of them so I can easily compare across them visually. Any help you can provide is much appreciated. Best, Kai -- 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/