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.

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/i nst/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. > > _______________________________________________ > 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 > >