[BioC] Join expression values of replicas in edgeR

Gordon K Smyth smyth at wehi.EDU.AU
Wed Apr 2 02:22:50 CEST 2014

Dear Maria,

Are you simply asking how to join sequencing libraries together?

If you have two matrices of counts (with the same number of rows 
representing the same genes or transcripts in the same order), then you 
can join them together using cbind:

   counts <- cbind(counts1, counts2)

Then make your DGEList as usual:

   d <- DGEList(counts=counts)


Best wishes

> Date: Mon, 31 Mar 2014 15:28:22 +0200
> From: Mar?a Jes?s Garc?a <mj.garcia.pereira at gmail.com>
> To: bioconductor at r-project.org
> Subject: [BioC] Join expression values of replicas in edgeR
> I'm working with RNAseq data and I would like to join the expression values
> for the replicas of the different treatments in edgeR. I would like to plot
> some figures with the combined information of my replicas, as I have found
> some confusing results when they are plotted invidually. Is there a way to
> do this in edgeR or maybe I could compute the mean expression value of
> samples over treatments and pass this matrix to edgeR?
> Thank you,
> -- 
> María Jesús García Pereira

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