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 f?r P?diatrie mit Schwerpunkt Neurologie Charit? - 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

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 f?r P?diatrie mit Schwerpunkt Neurologie > Charit? - 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