[BioC] problem with GDS2eSet

[Sean Davis]

On Mon, Jul 21, 2008 at 5:31 PM, Youngik Yang <yiyang at indiana.edu> wrote:
> Hi,
> I've got following error messages whenever I run GDS2eSet.
>
>> eset <- GDS2eSet(gds)
>
> File stored at:
> /tmp/Rtmpa4UdPv/GPL59.soft
> Error in validObject(.Object) :
>  invalid class "AnnotatedDataFrame" object:
>  AnnotatedDataFrame colnames of data differ from row.names of varMetadata
>
> The following lines were obtained by sessionInfo().
>
> R version 2.7.0 (2008-04-22)
> i386-redhat-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods [8]
> base
> other attached packages:
> [1] limma_2.9.17   GEOquery_2.2.1 RCurl_0.9-3    Biobase_1.12.2
>
> loaded via a namespace (and not attached):
> [1] biclust_0.5       flexclust_0.99-0  grid_2.7.0        lattice_0.17-6
>  [5] MASS_7.2-41       modeltools_0.2-15 stats4_2.7.0

Hello, Youngik.  You have some significant version mismatch between
your R version and bioconductor packages.  You should use biocLite()
to install the packages and upgrade GEOquery, Biobase, and potentially
many other packages.  If you still have problems, feel free to write
again.

Sean