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 -rw-rw-r-- 1 ivan ivan 9407867 2011-03-28 20:12 GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp 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. 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