[BioC] GEOquery not parsing GSE expression sets

[Maryvonne]

Sean Davis <sdavis2 at ...> writes:


> On Thu, Apr 4, 2013 at 12:09 PM, Lucas Santana dos Santos
> <santanasantosl at ...> wrote:
> > 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...
> 
> I'll look into it.  Thanks for the hint.
> 
> Sean
> 
>  Thanks,
>
> Lucas
>
> On Apr 4, 2013, at 12:00 PM, Sean Davis <sdavis2 at ...> wrote:
>
> On Thu, Apr 4, 2013 at 11:51 AM, Lucas Santana dos Santos
> <santanasantosl at ...> 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]]

Hi all!

I pull up this post because I got the same problem as Lucas. 
For some GSE I haven't any problem, and for some I have the 
following error:

Error in `row.names<-.data.frame`(`*tmp*`, value = value) : 
  invalid 'row.names' length

I let you the sessionInfo()

R version 3.0.2 (2013-09-25)
Platform: x86_64-redhat-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C 
 [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8
 [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] GEOmetadb_1.22.0   RSQLite_0.11.2     DBI_0.2-5          GEOquery_2.28.0
[5] Biobase_2.20.0     BiocGenerics_0.6.0

loaded via a namespace (and not attached):
[1] RCurl_1.95-4.1 XML_3.96-1.1

If someone has any solution to fix it or to understand what happens.

Thanks in advance

Maryvonne