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Maryvonne
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@maryvonne-6639
Last seen 11.1 years ago
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_s
eries_
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
