[BioC] Combining expressionSets from GEO

[Martin Morgan]

Hi Francois -- this might be related to a bug in Biobase that has been
fixed. Can you try to update your Biobase, either biocLite('Biobase')
or following the directions at http://bioconductor.org/download ? If
not, can you provide the output of traceback() after the error occurs?

Thanks,

Martin

Francois Pepin <fpepin at cs.mcgill.ca> writes:

> 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
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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