Hi. On Mon, Jun 27, 2011 at 8:37 AM, sean nj <njs...@gmail.com> wrote: > Hi guys, > > I am new to the aroma package and today I just followed the instuction on > Henrik et al's Feb 18, 2008 paper
This is "H. Bengtsson, R. Irizarry, B. Carvalho & T.P. Speed, Estimation and assessment of raw copy numbers at the single locus level, Bioinformatics 2008", correct? That paper describes the so called CRMA (v1) method. I strongly recommend that you use the CRMA v2 method for the more recent Affymetrix chip types such as GenomeWideSNP_6: H. Bengtsson, P. Wirapati & T.P. Speed, A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6, Bioinformatics, 2009. Available via http://aroma-project.org/publications/ There are vignettes for this chip type as well as the convenient one-line "block" method (http://aroma-project.org/blocks/), e.g. ds <- doCRMAv2("CCLE_Glioma_CN", chipType="GenomeWideSNP_6,Full", verbose=-10); > and tried my first test run. But I got the > following error message: > > Error in list(`process(acc)` = <environment>, > `process.AllelicCrosstalkCalibration(acc)` = <environment>, : > [2011-06-27 11:16:06] Exception: Failed to > retrieve genome information for this chip type: GenomeWideSNP_6 > I googled about this error message and found some people had similar error > before. I tried the suggestions like re-downloading the CDF, but it did not > help. > > Any suggestion? > > Thanks a lot for your help! > > Ying > > >> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full"); >> cdf > AffymetrixCdfFile: > Path: annotationData/chipTypes/GenomeWideSNP_6 > Filename: GenomeWideSNP_6,Full.cdf > Filesize: 470.44MB > Chip type: GenomeWideSNP_6,Full > RAM: 0.00MB > File format: v4 (binary; XDA) > Dimension: 2572x2680 > Number of cells: 6892960 > Number of units: 1881415 > Cells per unit: 3.66 > Number of QC units: 4 >> print(getChecksum(cdf)) > [1] "3fbe0f6e7c8a346105238a3f3d10d4ec" >> cs<-AffymetrixCelSet$byName("CCLE_Glioma_CN",chipType="GenomeWideSNP_6") If you do: cs <- AffymetrixCelSet$byName("CCLE_Glioma_CN", cdf=cdf) it should work. That will use the annotation data files that corresponds to the so called "full" CDF, i.e. annotation files named "GenomeWideSNP_6,Full,*" instead of the ones for the "default" CDF, i.e. "GenomeWideSNP_6,*". The above CRMA v2 paper describes the difference between "default" and "full" CDFs. >From you list of annotation files, here are the aroma ones that couple which each CDF: Default CDF (GenomeWideSNP_6.cdf): GenomeWideSNP_6,na31,hg19,HB20110328.ufl Note, if you want to use the "default" CDF, you also need to download the corresponding UGP file, which is actually what your current script is looking for. Full CDF (GenomeWideSNP_6,Full.cdf): "GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl" "GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp" Independent of CDF: "GenomeWideSNP_6,HB20080710.acs" None of the other annotation files you are listing are used by the aroma framework. Hope this helps /Henrik >> acc<-AllelicCrosstalkCalibration(cs) >> csC<-process(acc) > Error in list(`process(acc)` = <environment>, > `process.AllelicCrosstalkCalibration(acc)` = <environment>, : > > [2011-06-27 11:16:06] Exception: Failed to retrieve genome information for > this chip type: GenomeWideSNP_6 > at throw(Exception(...)) > at throw.default("Failed to retrieve genome information for this chip > type: ", chipType) > at throw("Failed to retrieve genome information for this chip type: ", > chipType) > at getGenomeInformation.AffymetrixCdfFile(cdf) > at getGenomeInformation(cdf) > at getSubsetToAvg.AllelicCrosstalkCalibration(this) > at getSubsetToAvg(this) > at getParameters.AllelicCrosstalkCalibration(this) > at getParameters(this) > at process.AllelicCrosstalkCalibration(acc) > at process(acc) >> sessionInfo() > R version 2.13.0 (2011-04-13) > Platform: i386-pc-mingw32/i386 (32-bit) > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 > [3] LC_MONETARY=English_United States.1252 > LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] aroma.cn_0.7.3 aroma.affymetrix_2.1.0 aroma.apd_0.1.8 > affxparser_1.24.0 > [5] R.huge_0.2.2 aroma.core_2.1.0 aroma.light_1.20.0 > matrixStats_0.2.2 > [9] R.rsp_0.5.4 R.cache_0.4.2 R.filesets_1.0.2 > digest_0.5.0 > [13] R.utils_1.7.5 R.oo_1.8.0 R.methodsS3_1.2.1 > > The following is a list of files in my > annotationData/chipTypes/GenomeWideSNP_6: > >> setwd("GenomeWideSNP_6") >> dir() > [1] "AFFX_README-NetAffx-CSV-Files.txt" > "GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl" > [3] "GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp" > "GenomeWideSNP_6,Full,specialSNPs" > [5] "GenomeWideSNP_6,Full.cdf" > "GenomeWideSNP_6,HB20080710.acs" > [7] "GenomeWideSNP_6,na31,annot.csv" > "GenomeWideSNP_6,na31,hg19,HB20110328.ufl" > [9] "GenomeWideSNP_6.birdseed-v2.models" > "GenomeWideSNP_6.birdseed.models" > [11] "GenomeWideSNP_6.brlmm-p.models" > "GenomeWideSNP_6.cdf" > [13] "GenomeWideSNP_6.chrXprobes" > "GenomeWideSNP_6.chrYprobes" > [15] "GenomeWideSNP_6.cif" > "GenomeWideSNP_6.grc" > [17] "GenomeWideSNP_6.psi" > "GenomeWideSNP_6.r2.qca" > [19] "GenomeWideSNP_6.r2.qcc" > "GenomeWideSNP_6.SMD" > [21] "GenomeWideSNP_6.specialSNPs" > "GenomeWideSNP6.na31.offstranderror.tab" >> > > -- > 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/
