[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:
http://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf
As far as getting data from GEO goes, the following would normally work
with GSE type records:
library(GEOquery)
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:
http://www.bioconductor.org/packages/release/bioc/html/Rsubread.html
And it's user guide:
http://www.bioconductor.org/packages/release/bioc/vignettes/Rsubread/inst/doc/Rsubread.pdf
Hope it helps,
Aliaksei.
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"
>
> --
> Sent via the guest posting facility at bioconductor.org.
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