how do you define "states"?

You might find the GEOmetadb package very useful.  Read the vignette for
it.  It may be what you need.

In terms of processing GSEs and GSMs, once you know what you are searching
for, it's much easier to find it.

Hope this helps.

--t



On Wed, Jul 24, 2013 at 10:55 AM, Lina Thomas [guest] <
guest@bioconductor.org> wrote:

>
> I am trying to work with GSE expression data from GEO in R using GEOquery.
>
> I am using the following commands
> gset <- getGEO("GSE52",GSEMatrix =TRUE,)
> ex <- exprs(gset[[1]])
>
> But I have no idea how to separate the data in two different states. I am
> trying to locate states data using
>
> varLabels(gset[[1]]@phenoData), when GSEMatrix =TRUE
>
> or
>
> Meta (gse), when GSEMatrix =FALSE
>
> But I still have no clue. I need to do this for around 1000 different
> database, so I cannot do it using GEO2R manually... Is there a particular
> field I can consider state?
>
> I also would like to know I can find out if data is already log2
> transformed or log10 or inits raw form using just R.
>
>  -- output of sessionInfo():
>
> none
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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