[BioC] GEOquery

[Sean Davis]

On Tue, Jul 22, 2008 at 10:53 AM, Florence Combes
<florence.combes at cea.fr> wrote:
> Dear Mister Davis,
>
> I am currently working as a bioinformatician in a public lab in Grenoble,
> France.
>
> I am using the GEOquery package to download data from A. thaliana that are
> stored in the GEO database.
> As I would like to get all the data for A. thaliana it is quite large, and I
> am interested in the 'GSEMatrix=TRUE' option, like here :
>
> gse.5738<-getGEO("GSE5738",GSEMatrix=TRUE)
>
> but I cannot see how to then access the processed data in the structure
> gse.5738. I have :
>
>
>> str(gse.5738)
> List of 1
>  $ GSE5738_series_matrix.txt.gz:Formal class 'ExpressionSet' [package
> "Biobase"] with 6 slots
>
> and all seems ok but nowhere I see values which seem to be processed
> microarray data.
>
> Would you mind give me a hint please ?

First, thanks for the interest in GEOquery.  Next, I think you might
want to update GEOquery to the latest version for your version of R
using the installation instructions on the bioconductor website (use
biocLite).

Now, to answer your question, gse.5738 is a list of ExpressionSet
objects.  In this case, it is a list of length 1.  You can get at the
ExpressionSet object itself by doing:

gse.5738[[1]]

This is an ExpressionSet and is one of the standard data structures
for microarray data in Bioconductor.  There is documentation about the
ExpressionSet class in the Biobase vignettes, which I encourage you to
look into.

Hope that helps,
Sean