Hi, Shawn.

On Thu, Oct 13, 2011 at 4:21 PM, Shawn Garbett [guest] <
guest@bioconductor.org> wrote:

>
> If I use GEOquery as follows:
>
> gse <- getGEO("GSE21259", GSEMatrix=TRUE)
>
> I get the following warnings after the load:
>
> Warning messages:
> 1: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) :
>  seek on a gzfile connection returned an internal error
> 2: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) :
>  seek on a gzfile connection returned an internal error
> 3: In readLines(con, 1) : seek on a gzfile connection returned an internal
> error
> 4: In read.table(file = file, header = header, sep = sep,  ... :
>  seek on a gzfile connection returned an internal error
> 5: In read.table(file = file, header = header, sep = sep,  ... :
>  seek on a gzfile connection returned an internal error
> 6: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) :
>  seek on a gzfile connection returned an internal error
> 7: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) :
>  seek on a gzfile connection returned an internal error
> 8: In readLines(con, 1) : seek on a gzfile connection returned an internal
> error
> 9: In read.table(file = file, header = header, sep = sep,  ... :
>  seek on a gzfile connection returned an internal error
> 10: In read.table(file = file, header = header, sep = sep,  ... :
>  seek on a gzfile connection returned an internal error
> 11: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) :
>  seek on a gzfile connection returned an internal error
> 12: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) :
>  seek on a gzfile connection returned an internal error
> 13: In readLines(con, 1) : seek on a gzfile connection returned an internal
> error
> 14: In read.table(file = file, header = header, sep = sep,  ... :
>  seek on a gzfile connection returned an internal error
> 15: In read.table(file = file, header = header, sep = sep,  ... :
>  seek on a gzfile connection returned an internal error
>
>
The warning messages are just that.  Things will work fine even with the
warnings.


> Then things that should work don't, i.e.:
>
> > GPLList(gse)
> Error in function (classes, fdef, mtable)  :
>  unable to find an inherited method for function "GPLList", for signature
> "list"
> > GSMList(gse)
> Error in function (classes, fdef, mtable)  :
>  unable to find an inherited method for function "GSMList", for signature
> "list"
>
> (1) Am I doing something wrong?
> (2) Is this data set on GEO broken in some way?
> (3) Or is it a bioconductor error?
>
>
You've got it most of the way.  The output of getGEO for a GSE when
GSEMatrix=TRUE is a *list* of ExpressionSets.  Try this:

names(gse)
gseEset = gse[[1]]
gseEset

You'll notice that gseEset is an ExpressionSet, so all the usual
ExpressionSet stuff "just works".

Hopefully that clarifies things.

Sean

P.S.  Thanks for sessionInfo().


>  -- output of sessionInfo():
>
> R version 2.13.2 (2011-09-30)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] GEOquery_2.19.4 Biobase_2.12.2
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.6-10 XML_3.4-3
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

