[BioC] GEOquery & GDS2eSet error

[Morten Mattingsdal]

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"