[BioC] How to use CRLMM with Affy 5.0 arrays

Benilton Carvalho bcarvalh at jhsph.edu
Tue Aug 26 13:08:51 CEST 2008


If you go to bioconductor's website or just use the biocLite tool,  
you'll be able to download the "right" pd.genomewidesnp.5 pkg.

Best, b.

On Aug 26, 2008, at 4:46 AM, Dominik Seelow  
<dominik.seelow at charite.de> wrote:

> Hello all,
>
> I'm trying to use the CRLMM algorithm to call genotypes on Affymetrix
> GenomeWideSNP 5.0 arrays.
> I create the respective pdInfo package with:
>
> library("pdInfoBuilder")
> cdfFile <- "GenomeWideSNP_5.cdf"
> csvAnno <- "GenomeWideSNP_5.na25.annot.csv"
> csvSeq <- "GenomeWideSNP_5.probe_tab"
> pkg <- new("AffySNPPDInfoPkgSeed", version = "0.1.5",
> author = "Seth Falcon", email = "sfalcon at fhcrc.org",
> biocViews = "AnnotationData", genomebuild = "NCBI Build 36",
> cdfFile = cdfFile, csvAnnoFile = csvAnno,
> csvSeqFile = csvSeq)
> makePdInfoPackage(pkg, destDir = ".")
>
> After installing the package and starting CRLMM, however, the oligo
> package complains that it could not find the 'table_info' table.
> The table structure in SQlite doesn't look the way it should:
>
>> conn <- db(pd.genomewidesnp.5)
>> dbListTables(conn)
> [1] "featureSet"    "mmfeature_tmp" "pm_mm"         "pmfeature_tmp"
> [5] "qcmmfeature"   "qcpm_qcmm"     "qcpmfeature"   "sequence"
>
> Any hints?
>
> TIA,
> Dominik
>
>
> --
> Dominik Seelow
> Klinik für Pädiatrie mit Schwerpunkt Neurologie
> Charité - Campus Virchow-Klinikum
> Augustenburger Platz 1
> D-13353 Berlin
> Germany
>
> phone   +49 30 450-566263
> fax     +49 30 450-566920
> e-mail  dominik.seelow at charite.de
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor



More information about the Bioconductor mailing list