[BioC] GEOquery and different GPL: handle of GSE
claudio.is at libero.it
claudio.is at libero.it
Thu Feb 8 10:59:41 CET 2007
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>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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