On Fri, Jul 24, 2009 at 9:11 AM, Manca Marco (PATH) <m.manca@path.unimaas.nl
> wrote:

>
> Dear Sean and dear bioconductors,
>
> I am writing you to ask a source of inspiration (code pieces, notes,
> references, whatever you might think appropriate) to import array annotation
> and other data from the GSE I am trying to work with (namely the GSE9820)
> into my eset.
>
> I have read on GEOquery's vignette that this is actually possible, despite
> being a bit tricky:
>
> "So, using a combination of lapply on the GSMList, one can extract as many
> columns of interest as necessary to build the data structure of choice.
> Because the GSM data from the GEO website are fully downloaded and included
> in the GSE object, one can extract foreground and background as well as
> quality for two-channel arrays, for example. Getting array annotation is
> also a bit more complicated, but by replacing \platform" in the lapply call
> to get platform information for each array, one can get other information
> associated with each array. Future work with this package will likely focus
> on better tools for manipulating GSE data" From
> http://www.bioconductor.org/packages/2.4/bioc/vignettes/GEOquery/inst/doc/GEOquery.pdfPage 22 of 22
>
> ...but I can't find anywhere any hint.
>
> Thank you in advance for your patience and support.
>

Hi, Marco.

Have you tried:

gse <- getGEO('GSE9820')[[1]]

This should get you all the annotation and the normalized (according to the
original submitter's methods) data in an ExpressionSet.  If that isn't what
you need, could you please provide the output of sessionInfo(), the code you
have tried, and what shortcomings your code has?

Thanks,
Sean

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