Hi Henrik, I tried CRMAv2 and it went successfully.
Thanks a lot for the help! Ying On Mon, Jun 27, 2011 at 5:18 PM, Henrik Bengtsson < henrik.bengts...@aroma-project.org> wrote: > 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/ > -- 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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