[BioC] GEOquery and different GPL: handle of GSE

[claudio.is at libero.it]

---------- Initial Header -----------

>From      : "Sean Davis" sdavis2 at mail.nih.gov
To          : "claudio.is at libero.it" claudio.is at libero.it
Cc          : "bioconductor" bioconductor at stat.math.ethz.ch
Date      : Wed, 07 Feb 2007 21:28:21 -0500
Subject : Re: [BioC] GEOquery and different GPL: handle of GSE

I will show you the script for another GSE accession I have it right now, 

library(GEOquery)
library(Biobase)

#downloading and storing in GSE
gse2564=getGEO("GSE2564")

#Check for GPL of each platform
gsmplatforms <- lapply(GSMList(gse2564), function(x) {
 Meta(x)$platform
 })


## now I wanted to sub-index the gse according to the field $platoform, and as when I run 


GSMList(gse2564)[1]

the object is a GSM, I suppose that the following line should works

GSMList(gse2564)[1]$platform

but I retrive a null results.


> claudio.is at libero.it wrote:
> > Dear BioC,
> >
> > I'm downloading a dataset from NCBI GEO with GEOquery, in particular GSE3654, which is composed by different GPL platforms; according to the vignette I have to split the dataset according to the GPLs, but I found I was not able to handle the GSE classes and sub-index it. Can you help me?
> >   
> Claudio,
> 
> I'm glad to hear you have gotten the data downloaded and into a GSE 
> object.  In what column of the GSM tables are you interested?  Also, 
> what have you tried?  I can comment more fully with that information.
> 
> Sean
> 


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