Hi. On Tue, Oct 25, 2011 at 9:22 AM, Ivan Smirnov <vanya...@gmail.com> wrote: > Hi Pierre, thanks for prompt reply, however I do have all those > annotation files downloaded from that link, see below. Do I need to > rename them (e.g. remove tags)? > > /aroma.exon: ls -l annotationData/chipTypes/GenomeWideSNP_6 > total 1099456 > -rw-r--r-- 1 ivan ivan 493291745 2011-10-23 20:03 GenomeWideSNP_6,Full.cdf > -rw-rw-r-- 1 ivan ivan 179217531 2008-07-17 17:43 > GenomeWideSNP_6,Full,HB20080710.acs > -rw-rw-r-- 1 ivan ivan 436492121 2011-10-24 15:34 > GenomeWideSNP_6,Full,monocell.CDF
> -rw-rw-r-- 1 ivan ivan 7424585 2011-03-28 20:14 > GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl >From the file size, it seems as if you have downloaded GenomeWideSNP_6,na31,hg19,HB20110328.ufl and renamed it to have a "Full" tags, because GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl should be 7,526,452 bytes. Could this be it? > -rw-rw-r-- 1 ivan ivan 9407867 2011-03-28 20:12 > GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp Also, what is your sessionInfo()? /Henrik > > Thanks > Ivan > > On Tue, Oct 25, 2011 at 2:09 AM, <aroma-affymetrix@googlegroups.com> wrote: >> Today's Topic Summary >> >> Group: http://groups.google.com/group/aroma-affymetrix/topics >> >> Problem with doCRMAv2 [2 Updates] >> >> Problem with doCRMAv2 >> >> Ivan Smirnov <vanya...@gmail.com> Oct 24 04:35PM -0700 >> >> Hi Henrik, >> >> I am trying to run the script: >> >> options(echo = FALSE,digits=4) >> library(aroma.affymetrix) >> verbose <- Verbose(threshold=-8, timestamp=TRUE); >> dataSet="Gupta_CC" >> chipType <- "GenomeWideSNP_6" >> cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full"); >> print(cdf) >> dsList <- doCRMAv2(dataSet, cdf=cdf, combineAlleles=FALSE, verbose=verbose); >> dsC <- dsList$total; >> print(dsC); >> >> >> and it is crushing with: >> >> 20111024 16:05:12| Normalizing set for PCR fragment-length effects... >> 20111024 16:05:12| Identifying SNP and CN units... >> types >> 1 2 5 >> 621 934968 945826 >> 20111024 16:05:13| subsetToUpdate: >> int [1:1880794] 622 623 624 625 626 627 628 629 630 631 ... >> 20111024 16:05:13| Identifying SNP and CN units...done >> 20111024 16:05:13| Retrieving SNP information annotations... >> 20111024 16:05:13| Defining DChipSnpInformation from chip type... >> 20111024 16:05:13| Chip type: GenomeWideSNP_6 >> 20111024 16:05:13| Version: >> 20111024 16:05:13| Located pathname: >> 20111024 16:05:13| Defining DChipSnpInformation from chip type...done >> Error in list(`doCRMAv2(dataSet, cdf = cdf, combineAlleles = FALSE, >> verbose = verbose)` = <environment>, : >> >> [2011-10-24 16:05:13] Exception: Failed to retrieve SNP information >> for this chip type: GenomeWideSNP_6 >> at throw(Exception(...)) >> at throw.default("Failed to retrieve SNP information for this chip type: ", >> ch >> at throw("Failed to retrieve SNP information for this chip type: ", >> chipType) >> at getSnpInformation.AffymetrixCdfFile(cdf) >> at getSnpInformation(cdf) >> at process.FragmentLengthNormalization(fln, verbose = verbose) >> at process(fln, verbose = verbose) >> at doCRMAv2.AffymetrixCelSet(csR, ..., verbose = verbose) >> at doCRMAv2(csR, ..., verbose = verbose) >> at doCRMAv2.character(dataSet, cdf = cdf, combineAlleles = FALSE, verbose = >> ve >> at doCRMAv2(dataSet, cdf = cdf, combineAlleles = FALSE, verbose = verbose) >> Calls: doCRMAv2 ... getSnpInformation.AffymetrixCdfFile -> throw -> >> throw.default -> throw -> throw.Exception >> 20111024 16:05:13| Retrieving SNP information annotations...done >> 20111024 16:05:13| Normalizing set for PCR fragment-length effects...done >> Execution halted >> >> >> So, it seems to have problem getting info from CDF file. But >> print(cdf) looks normal: >> >> 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 >> >> and the check sum is identical to one posted on the web: >> "3fbe0f6e7c8a346105238a3f3d10d4ec" >> >> All my software is up to date. Any clues? >> >> Thanks >> Ivan >> >> >> >> Pierre Neuvial <pie...@stat.berkeley.edu> Oct 25 02:35AM +0200 >> >> Hi Ivan, >> >>> 20111024 16:05:13| Version: >>> 20111024 16:05:13| Located pathname: >>> 20111024 16:05:13| Defining DChipSnpInformation from chip type...done >> >> Do you have UGP and UFL annotation files in your >> annotationData/chipTypes/GenomeWideSNP_6 ? From the above error it >> looks like >> instead you have (very) old SNP annotation files, which are not used >> anymore within the Aroma Project, cf >> >> http://www.mail-archive.com/aroma-affymetrix@googlegroups.com/msg01456.html >> >> If you don't have UGP and UFL annotation files, please download them from >> >> http://www.aroma-project.org/chipTypes/GenomeWideSNP_6 >> >> Hope this helps, >> >> Pierre. >> >> >> >> >> You received this message because you are subscribed to the Google Group >> aroma-affymetrix. >> You can post via email. >> To unsubscribe from this group, send an empty message. >> For more options, visit this group. >> >> -- >> 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. 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/
