Hi all, I am using aroma.affymetrix to get the segmented paired copy numbers for raw CELL files and CDF annotation files. The path and the R script are shown below. As you can see in the result table, the last column is showing a link to UCSC browser that indicates hg 18 is used which I wasn't expecting this because I used hg 19 as the annotation file. Please let me know if this is ok? Because I am getting some errors for my downstream analysis and I wonder it might be because of this.
<https://lh6.googleusercontent.com/-2b-ttHBkbq8/UOS9vGSF6oI/AAAAAAAAACQ/7ewachBquZ8/s1600/Untitled.png> rawData/ Lee10Lung/ GenomeWideSNP_6/ TCGA-06-0158-01A-01D-1491-08.5.CEL TCGA-06-0158-10A-01D-1491-08.5.CEL annotationData/ chipTypes/ GenomeWideSNP_6/ GenomeWideSNP_6,Full,HB20080710.acs GenomeWideSNP_6,Full,monocell.CDF GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp GenomeWideSNP_6,Full.cdf GenomeWideSNP_6,Full.cdf.bin #### R script: >dataSet <-"TCGA-06-0158"; >chipType <-"GenomeWideSNP_6"; >chiptags <-"Full"; >library(aroma.affymetrix) >verbose <- Arguments$getVerbose(-8, timestamp=TRUE); >options(digits=4); #---------------------------------------------------------------------- ##Number of CEL files #---------------------------------------------------------------------- >cdf <-AffymetrixCdfFile$byChipType(chipType, tags=chiptags); >csR <-AffymetrixCelSet$byName(dataSet, cdf=cdf); >n <-length(getNames(csR)) #---------------------------------------------------------------------- ## # Results from doCRMAv2 TRUE >dsC <- doCRMAv2(dataSet, cdf=cdf, verbose=verbose); >print(dsC); AromaUnitTotalCnBinarySet: Name: TCGA-06-0158 Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY Full name: TCGA-06-0158,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY Number of files: 2 Names: TCGA-06-0158-01A-01D-1491-08.5, TCGA-06-0158-10A-01D-1491-08.5 [2] Path (to the first file): totalAndFracBData/TCGA-06-0158,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6 Total file size: 14.35 MB RAM: 0.00MB ##--------------------------------------------- #Split data set in (tumor, normal) pair ##--------------------------------------------- >idxT <- match("TCGA-06-0158-01A-01D-1491-08.5", getNames(dsC)); >dsT <- extract(dsC, idxT); >idxN <- match("TCGA-06-0158-10A-01D-1491-08.5", getNames(dsC)); >dsN <- extract(dsC, idxN); ##------------------- ## Setting up a paired CBS model ##------------------- >cns <- CbsModel(dsT, dsN); # Perform CBS segmentation for all chromosomes >fit(cns, verbose=verbose); ##------------------- ## EXTRACT SEGMENTATION RESULTS ##------------------- >regDatList <-getRegions(cns) >write.table(regDatList, file="seg_2_0158_2.txt", sep="\t", quote=F) >sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] DNAcopy_1.30.0 sfit_0.1.9 aroma.affymetrix_2.7.0 [4] affxparser_1.28.1 aroma.apd_0.2.3 R.huge_0.4.1 [7] aroma.light_1.24.0 aroma.core_2.7.0 matrixStats_0.6.2 [10] R.rsp_0.8.2 R.devices_2.1.3 R.cache_0.6.5 [13] R.filesets_1.6.0 digest_0.6.0 R.utils_1.18.0 [16] R.oo_1.10.1 R.methodsS3_1.4.2 loaded via a namespace (and not attached): [1] PSCBS_0.30.0 tools_2.15.1 -- 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 [email protected] To unsubscribe and other options, go to http://www.aroma-project.org/forum/
