[BioC] Combining expressionSets from GEO

[Francois Pepin]

Hi everyone,

I'm getting an error message when trying to combine two parts of a GSE
object:

>tmp<-getGEO('GSE3526',GSEMatrix=T)
> tmp2<-combine(tmp[[1]],tmp[[2]])
Error in alleq(levels(x[[nm]]), levels(y[[nm]])) && alleq(x
[sharedRows,  :
  invalid 'x' type in 'x && y'

Checking to make sure that I should be able to combine them (from the
eSet documentation):

#eSets must have identical numbers of 'featureNames'
> all(featureNames(tmp[[2]])==featureNames(tmp[[2]]))
[1] TRUE

#must have distinct 'sampleNames'
> any(sampleNames(tmp[[1]])%in%sampleNames(tmp[[2]]))
[1] FALSE

#and must have identical 'annotation'.
> annotation(tmp[[2]])==annotation(tmp[[2]])
[1] TRUE

> sessionInfo()
R version 2.6.0 (2007-10-03)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] GEOquery_2.2.0 RCurl_0.8-1    Biobase_1.16.0

loaded via a namespace (and not attached):
[1] rcompgen_0.1-15

Does anyone know why that is happening and if there would be any way
around it?

Francois