Hi, Maryvonne.


On Wed, Jul 9, 2014 at 11:25 AM, Maryvonne <
maryvonne.merletbillon@hotmail.fr> wrote:

>
>
> Sean Davis <sdavis2@...> writes:
>
>
> > On Thu, Apr 4, 2013 at 12:09 PM, Lucas Santana dos Santos
> > <santanasantosl@...> 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@...> wrote:
> >
> > On Thu, Apr 4, 2013 at 11:51 AM, Lucas Santana dos Santos
> > <santanasantosl@...> 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
>

Can you include an example where you get this error?  It makes it a bit
easier to track down.


>
> I let you the sessionInfo()
>
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-redhat-linux-gnu (64-bit)
>
>
Looks like you might need to update your R/Bioc version.

Sean



> 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
>
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	[[alternative HTML version deleted]]

