Dear Henrik, thank you so much for your complete answer! I'll try your suggestions on monday and give you some feedback!
Best, Xavi. 2011/6/17 Henrik Bengtsson <henrik.bengts...@aroma-project.org> > Hi. > > On Thu, Jun 16, 2011 at 9:52 AM, Xavi Sole <xavier.s...@gmail.com> wrote: > > 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); > > No need for 'aroma.cn' here. > > > 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"; > > Each analysis you run should have a unique data set name, i.e. what > name should you use next time? I recommend to use a much more > informative name of your data set - something that reflects the > project name and/or the investigator and the year, or similar. > > > dsR <- AffymetrixCelSet$byName(dataSet, cdf=cdf); > > setFullName(dsR, dataSet); > > No need to do this. > > > # Using CRMAv2 > > dsList <- doCRMAv2(dataSet, cdf=cdf, combineAlleles=FALSE, > verbose=verbose); > > Since you've already have setup an AffymetrixCelSet object ('dsR') > above, you should use that instead: > > dsList <- doCRMAv2(dsR, combineAlleles=FALSE, verbose=verbose); > > or even shorter for allele-specific analysis, you can equivalently do: > > dsList <- doASCRMAv2(dsR, verbose=verbose); > > > dsC <- dsList$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"); > > This is a bit dangerous since it assumes that the rows in your > 'samples.txt' file is ordered the same way as the files on this. At > least I would assert that that is the case by something like: > > stopifnot(all(infoSamples$name == getName(dsC)); > > or similar. > > > 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); > > Yes, this does a tumor-normal paired CBS segmentation (and extracts > the table of regions afterward). > > > # 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); > > This is the correct command and 'avgN' should *indeed* a single file > ("array") here. You should be able verify by looking at what: > > print(avgN); > > returns. > > > cns.unpaired <- CbsModel(dsT, avgN); > > This should work, because 'dsT' is a data set; verify by > > print(dsT); > > If it doesn't work please let us know what: > > print(dsT); > print(avgN); > > returns and what the complete error message is. > > > fit(cns.unpaired, verbose=TRUE); > > regDatList.unpaired <- getRegions(cns.unpaired); > > [snip] > > I'll answer your second question in a separate thread ...and when I > find the time. > > /Henrik > > > 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/ > > > > -- > 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. 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