[BioC] mRNA-seq cross-species analysis, is it possible?

Thomas J Hardcastle tjh48 at cam.ac.uk
Thu Aug 4 12:45:37 CEST 2011

> ----------------------------------------------------------------------
> Message: 5
> Date: Wed, 3 Aug 2011 14:48:28 +0100
> From: mali salmon <shalmom1 at gmail.com>
> To: bioconductor at r-project.org
> Subject: [BioC] mRNA-seq cross-species analysis, is it possible?
> Message-ID:
> 	<CAH5dN6xgOkWmjdjMpmMRBV4iykz4nZC7PyJrKUfAHgCkQGhMPA at mail.gmail.com>
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> Dear list
> I would like to perform mRNA-seq cross-species comparison. In that case it
> would be necessary to account for the differences in gene length.
> I already got a reply from the author of DESeq (see below) that this is
> currently can't be done with DESeq.
> Is it possible to specify gene-specific normalization factor with edgeR? or
> to input read counts that have been normalized to gene length?
> Thanks
> Mali
Hi Mali,

It's also possible to use baySeq to analyse samples with different gene 
lengths. If you look at section 7 of the vignette for this package, you 
will see the 'seglens' slot of a countData object being given as a 
vector. In this case, baySeq uses, for each gene, the same length across 
all samples. However, you can instead pass a matrix to the seglens slot, 
of the same dimensions as your 'data' vector, that will use different 
gene lengths for different samples.

For example, if the first gene were of length 1000 in one species, and 
2500 in the other species, and you have two replicates of each 
condition, the first row of the seglens slot should be:
[,1] 1000, 1000, 2500, 2500

Analysis then proceeds as normal.


Dr. Thomas J. Hardcastle

Department of Plant Sciences
University of Cambridge
Downing Street
Cambridge, CB2 3EA
United Kingdom

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