Sergii Ivakhno wrote:
> Dear Biocondcutor users
> Can someone help me with the following problem?
> I use GEO query to fetch a GDS record from GEO and then I use
GDS2eSet to export it into exppressionset. According to the source
code GDS2eSet also retrieves GPL record
> if(is.null(GPL)) {
> GPL <- getGEO(Meta(GDS)$platform)
> }
>
> When the GPL is downloaded I get the following error:
> File stored at:
> /tmp/RtmpMbEluC/GPL570.soft
> Error in validObject(.Object) : invalid class "AnnotatedDataFrame"
object:
> AnnotatedDataFrame colnames of data differ from row.names of
varMetadata
> Execution halted
>
> Interestingly, but I do not get this error on Windows (only linux)
> Thanks a lot in advance.
>
Hi, Sergii. Could you let me know what version you are using by
giving
sessionInfo()?
Thanks,
Sean
Sergii Ivakhno wrote:
> Thanks Sean,
> The version is:
> R version 2.4.0 (2006-10-03)
> x86_64-unknown-linux-gnu
> locale:
>
> attached base packages:
> [1] "methods" "stats" "graphics" "grDevices" "utils"
"datasets"
> [7] "base"
>
Thanks, Sergii. But what versions of GEOquery and Biobase are you
using?
Sean
