Hi. On Thu, Jan 3, 2013 at 12:11 AM, Saman Amini <[email protected]> wrote: > > 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.
It's all ok. The generated "hg18" string is (still) hardcoded into the code and is independent of any "hg" tags/information you have in your annotation files. How to get "hg19", see https://groups.google.com/d/msg/aroma-affymetrix/r8CtCvdGWnE/jzQFMifxt2MJ - the summary is that: "You can rewrite the regions.xls file with the correct UCSC Genome Browser by passing argument 'hgVersion' (defaults to "hg18"): process(ce, hgVersion="hg19") To recreate the regions.xls file afterward, do: writeRegions(ce, hgVersion="hg19") or just do a search/replace in an editor." Hope this helps /Henrik > > > > > 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/ -- 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/
