[BioC] GEOquery not parsing GSE expression sets

[Lucas Santana dos Santos]

Hi Sean,

I think I might know the source of error. GEOquery works fine before I load the 'mvbutils' package. 
Once I load it I starting getting the error...

Thanks,

Lucas 

On Apr 4, 2013, at 12:00 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:

> 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
>>        [[alternative HTML version deleted]]
>> 
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