Hi Sean,

Thanks for your answer!

That is great already.

I can see the gene's names now:

> library(GEOquery)
> gset <- getGEO("GSE11024", GSEMatrix=TRUE, AnnotGPL=TRUE)
> head(fData(gset[[1]]))$Gene
[1] A1BG NAT2 ADA  CDH2 AKT3 MED6
17098 Levels:  A1BG ABCB6 ABCC5 ABCC9 ABCF2 ABI1 ACOT8 ACTR2 ACTR3 ADA
ADAM8 AKT3 ... ZNF254

But the data frame only contains these columns.

> names(fData(gset[[1]]))
 [1] "ID"           "Gene"         "UniGene"      "Description"  "Ensembl*
Chr" "Start (bp)"
 [7] "End (bp)"     "Strand"       "ORF"          "SPOT_ID"

Where is the expression information for each gene?

Thanks,
Marcelo



On Thu, May 8, 2014 at 6:24 AM, Sean Davis <sdavis2@mail.nih.gov> wrote:

> Hi, Marcelo.
>
>
> On Wed, May 7, 2014 at 8:01 PM, Marcelo Pereira <marcelops@gmail.com>
> wrote:
> > Quick question:
> >
> > I am trying to import some GEO datasets, and having some issues with the
> > annotations:
> >
> > I can download the GSE dataset using:
> >
> > gset <- getGEO("GSE11024", GSEMatrix=TRUE, AnnotGPL=TRUE)
> >
> >
> > However, it will return me a ExpressionSet with the following format:
> >
> >               X1    X10    X100   X1000 ...
> > GSM278765
> > GSM278766
> > GSM278767
> > GSM278768
> > GSM278769
> > ...
>
> This is not what is returned by GEOquery, so you have done some
> manipulation (looks like you did a transpose on the expression
> matrix), it seems.
>
> > This is pretty much what I need, but I still need to translate (X1, X10,
> > X100, X1000, etc...) to the actual names of the genes.
>
> library(GEOquery)
> gset <- getGEO("GSE11024", GSEMatrix=TRUE, AnnotGPL=TRUE)[[1]]
> head(fData(gset))
>
> The gene symbols are in the "Gene" column:
>
> genesymbols = fData(gset)$Gene
>
> Sean
>
>
> >
> > Any suggestions?
> >
> > Thanks,
> > Marcelo
> >
> >         [[alternative HTML version deleted]]
> >
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