[BioC] RNA seq

Aliaksei Holik salvador at bio.bsu.by
Tue Apr 22 05:37:30 CEST 2014

Hi Minni,

I presume you know, how to analyse RNAseq data and you're only stuck 
with getting the data from the GEO repository. If I'm incorrect  and you 
don't know how to analyse RNAseq data, I'd suggest you read through 
edgeR User Guide:

As far as getting data from GEO goes, the following would normally work 
with GSE type records:

getGEO(GEO="GSE12946", destdir=".", AnnotGPL=T)
GSE12946.data <- getGEO(filename="GSE12946_series_matrix.txt.gz")

This would give you an expressionSet object, including annotation, from 
which you can extract expression data, gene annotation and sample 
annotation as follows:
exprs(GSE12946.data) # Expression values
fData(GSE12946.data) # Feature annotation
pData(GSE12946.data) # Sample annotation

Unfortunately, in your case the resulting object appears to be empty, 
i.e. there's no actual expression values in it. This doesn't seem to 
have anything to do with getGEO, as even if you download the series 
matrix manually, there's no expression data in there either. You may 
wish to get in touch with the authors and ask them to upload the 
processed data. Alternatively, you can download the raw data for this 
submission from GEO. I imagine this would be raw read files and you'd 
need to do the mapping and counting before you can do differential 
expression analysis, in which case I'd refer you to Rsubread package:
And it's user guide:

Hope it helps,


On 22/04/14 12:57 PM, Minni [guest] wrote:
> I am a beginner of R studio. I downloaded the annotation data by using this command:
>> annoation(gse), >platf<-getGEO(annotation(gse),AnnotGPL=TRUE), which I got stuck for the next step. My main goal is to get the differential genes from GSE12946 (RNA-seq). Please guide me through it. Thanks
>   -- output of sessionInfo():
> annotation(gse)
> [1] "GPL9052"
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