Hello everyone, Im using GEOquery to retriveve several breast cancer datasets from the GEO database. The conversion to the LIMMA object MA goes fine for two-color data, but Im having difficulties with making an exprSet from the affymetrix data retrieved. The function GDS2eSet returns: "Error in validObject(.Object) : invalid class "exprSet" object: sampleNames different from names of phenoData rows" I have tried several different datasets and this error seems very common. Is this an annotation problem in the GEO database or my fault ? NB Im aware that GEOquery in the development section of BioC, and im sorry if support of devel. packages is not included in the mailinglist some help is greatly appriciated though morten my code: library(GEOquery) library(Biobase) # 2 channel -> LIMMA MA object GDS807<- getGEO("GDS807", destdir=".") Meta(GDS807)$channel_count MA <- GDS2MA(GDS807) #1 channel -> affy eset object GDS1250<- getGEO("GDS1250", destdir=".") Meta(GDS1250)$channel_count eset <- GDS2eSet(GDS1250,do.log2=TRUE) Error in validObject(.Object) : invalid class "exprSet" object: sampleNames different from names of phenoData rows > sessionInfo() Version 2.3.0 Under development (unstable) (2006-02-01 r37236) i386-pc-mingw32 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" "datasets" "base" other attached packages: limma GEOquery AnnBuilder RSQLite DBI XML annotate Biobase mgug4121a "2.4.9" "1.5.3" "1.9.11" "0.4-1" "0.1-10" "0.99-6" "1.9.2" "1.9.5" "1.10.0"

On 2/14/06 10:30 AM, "Morten Mattingsdal" <morten.mattingsdal at="" student.uib.no=""> wrote: > Hello everyone, > Im using GEOquery to retriveve several breast cancer datasets from the > GEO database. > The conversion to the LIMMA object MA goes fine for two-color data, but > Im having difficulties with making an exprSet from the affymetrix data > retrieved. The function GDS2eSet returns: > > "Error in validObject(.Object) : invalid class "exprSet" object: > sampleNames different from names of phenoData rows" > > I have tried several different datasets and this error seems very common. > Is this an annotation problem in the GEO database or my fault ? Not your fault. This is due to a recent change in the way that exprSets validate their slots when creating a new exprSet object. I have fixed the problem and committed the changes to BioConductor. They should be available in the next 24 hours or so in the development repository. Sean