[BioC] GEOquery not parsing GSE expression sets

[Sean Davis]

On Thu, Apr 4, 2013 at 11:51 AM, Lucas Santana dos Santos
<santanasantosl at me.com> wrote:
> All,
>
> I have been trying to use the function getGEO, part of GEOquery package to retrieve GSE objects.
> However, I am getting the following error message:
>
> data/GEO> gse2553 <- getGEO('GSE2553',GSEMatrix=TRUE)
> Found 1 file(s)
> GSE2553_series_matrix.txt.gz
> Using locally cached version: /var/folders/z4/hzbhqd1j3gzc4mqhq29fqb240000gr/T//Rtmpb3s3hN/GSE2553_series_matrix.txt.gz
> Error in `row.names<-.data.frame`(`*tmp*`, value = value) :
>  invalid 'row.names' length
>
> I get the same error no matter which GEO GSE id I use. It seems to be a parsing error, when creating a data frame
> This was suppose to work, as this code snippet is from the "Using the GEOquery package" PDF (page 13: http://www.bioconductor.org/packages/2.11/bioc/vignettes/GEOquery/inst/doc/GEOquery.pdf).
>
> Any thoughts about what id the cause of error or how to fix it?

Hi, Lucas.

Could you send the output of sessionInfo()?  Also, could you try this
in a new R session?  It appears that GEOquery is picking up a cached
version of the series matrix file that might be corrupted.

Sean

>
> Thank you very much,
>
>
> Lucas
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>
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