[BioC] How to use CRLMM with Affy 5.0 arrays

Dominik Seelow dominik.seelow at charite.de
Tue Aug 26 10:46:02 CEST 2008

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:

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?


Dominik Seelow
Klinik für Pädiatrie mit Schwerpunkt Neurologie
Charité - Campus Virchow-Klinikum
Augustenburger Platz 1
D-13353 Berlin

phone   +49 30 450-566263
fax     +49 30 450-566920
e-mail  dominik.seelow at charite.de

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