Hi all, I have successfully performed CRMAv2 on a set of ~200 Affy 6.0 samples. I have tumor and normal samples, and now I want to apply an unpaired CBS model. I know ho to do the paired model, but I'm not sure is this code is right for the unpaired one:
library(aroma.affymetrix); library(aroma.cn); verbose <- Arguments$getVerbose(-8, timestamp=TRUE); options(digits=4); setOption(aromaSettings, "memory/ram", 500.0) # Verify that the data set can be located: cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full"); dataSet <- "CEL_files"; dsR <- AffymetrixCelSet$byName(dataSet, cdf=cdf); setFullName(dsR, dataSet); # Using CRMAv2 dsList <- doCRMAv2(dataSet, cdf=cdf, combineAlleles=FALSE, verbose=verbose); dsC <- dsList$total; # Splitting the dataset in normal-tumor pairs infoSamples <- read.table("samples.txt", sep="\t", header=TRUE, as.is=TRUE, strip.white=TRUE); #Rows in this file are in the same order as arrays in the aroma dataset. idxN <- which(infoSamples$type=="Normal"); idxT <- which(infoSamples$type=="Tumor"); dsN <- extract(dsC, idxN); dsT <- extract(dsC, idxT); # Circular binary segmentation T vs N: Paired model (first N sample pairs with first T sample) cns <- CbsModel(dsT, dsN); fit(cns, verbose=TRUE); regDatList <- getRegions(cns); # Circular binary segmentation T vs N: Unpaired: I DON'T KNOW IF THIS IS CORRECT (cns.unpaired keeps me telling that the reference sample is made of 102 files instead of one!). avgN <- getAverageFile(dsN); cns.unpaired <- CbsModel(dsT, avgN); fit(cns.unpaired, verbose=TRUE); regDatList.unpaired <- getRegions(cns.unpaired); Besides that, another doubt I have is how to extract raw total copy numbers into a tab-delimited file after applying doCRMA. Is this code correct? I assume these CN values are normalized, aren't they? dataSet <- "CEL_files"; tags <- "ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY"; chipType <- "GenomeWideSNP_6"; ds <- AromaUnitTotalCnBinarySet$byName(dataSet, tags=tags, chipType=chipType); dfTxt <- writeDataFrame(ds, columns=c("unitName", "chromosome", "position", "*")); print(dfTxt); If I wanted to extract allele-specific CN is it enough to change tags <- "ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY"; to tags <- "ACC,ra,-XY,BPN,-XY,A+B,FLN,-XY"; ? Thank you very much for your help! Best, Xavi. #SESSION INFO > sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] DNAcopy_1.26.0 aroma.cn_0.5.2 aroma.affymetrix_2.1.0 [4] aroma.apd_0.1.8 affxparser_1.24.0 R.huge_0.2.2 [7] aroma.core_2.1.0 aroma.light_1.20.0 matrixStats_0.2.2 [10] R.rsp_0.5.3 R.cache_0.4.2 R.filesets_1.0.1 [13] digest_0.5.0 R.utils_1.7.5 R.oo_1.8.0 [16] R.methodsS3_1.2.1 loaded via a namespace (and not attached): [1] tools_2.13.0 -- 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/