[BioC] Adding annotations to GSE datasets

[Sean Davis]

Hi, Marcelo.


On Wed, May 7, 2014 at 8:01 PM, Marcelo Pereira <marcelops at 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]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor