Dear Ingunn,
Once the data has been summarized as counts for transcripts, the edgeR
package will do a good job of differential expression between
conditions,
assuming there are some replicates.
Best wishes
Gordon
> Date: Thu, 12 Feb 2009 10:18:17 +0100
> From: Ingunn Berget <ingunn.berget at="" umb.no="">
> Subject: [BioC] Analysing RNA-seq data
> To: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch="">
>
> Are there any packages in Bioconductor for analysing RNA-seq data?
>
>
> Ingunn Berget (Dr. Scient)
> UMB, box 5003, IHA
> 1432 ?s
> Norway
>
> Centre for Integrative Genetics, www.cigene.no
> Centre for Biospectroscopy and Data Modelling, www.specmod.org
Based on my experience, after a certain transformation, e.g.
log(x+0.5), (+0.5 to avoid log(0) for the count x) either SAM or limma
will perform well. I think the permutation method is necessary for
p-value evaluation.
Best,
Yinglei
----- Original Message -----
From: Gordon K Smyth <smyth@wehi.edu.au>
Date: Thursday, February 12, 2009 5:31 pm
Subject: [BioC] Analysing RNA-seq data
To: Ingunn Berget <ingunn.berget at="" umb.no="">
Cc: Bioconductor mailing list <bioconductor at="" stat.math.ethz.ch="">
> Dear Ingunn,
>
> Once the data has been summarized as counts for transcripts, the
edgeR
>
> package will do a good job of differential expression between
> conditions,
> assuming there are some replicates.
>
> Best wishes
> Gordon
>
> > Date: Thu, 12 Feb 2009 10:18:17 +0100
> > From: Ingunn Berget <ingunn.berget at="" umb.no="">
> > Subject: [BioC] Analysing RNA-seq data
> > To: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch="">
> >
> > Are there any packages in Bioconductor for analysing RNA-seq data?
> >
> >
> > Ingunn Berget (Dr. Scient)
> > UMB, box 5003, IHA
> > 1432 ?s
> > Norway
> >
> > Centre for Integrative Genetics, www.cigene.no
> > Centre for Biospectroscopy and Data Modelling, www.specmod.org
>
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