Dear all,
I am analyzing RNA-seq data generated from liver samples in two species, 
human and chimp, with 4 biological replicates in each species. I have 
mapped the reads to 1-to-1 orthologous exons, and I'm aiming at 
detecting DE exons between species. After reading the "voom" paper 
(http://www.statsci.org/smyth/pubs/VoomPreprint.pdf), I am leaning 
towards using this approach rather than count-based approaches like 
edgeR or DESeq.

One problem that I encounter is that orthologous exons in human and 
chimp don't always have the same length, so I was looking for some way 
to correct for exon length when testing for DE. In the voom paper it is 
mentioned that although voom is based on log-cpm values, it "/can work 
however just as easily with logged RPKM values in place of log-cpm, 
because the precision weights are the same for both measures. If the 
genomic length of each gene is known, then the log-cpm values output by 
voom can be converted to log-RPKM by subtracting the log-base-2 gene 
length in kilobases. The downstream analysis is unchanged and will yield 
identical results in terms of differentially expressed genes and 
estimated fold changes/."

But I think this comment applies to comparisons across genes (e.g., when 
all samples from an experiment are from the same species), while in my 
case I wanted to use RPKMs to normalize for differences in gene lengths 
between samples.
Did I miss something? Would you have any advice on how to proceed?

Thanks a lot for your help
Julien


 > sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] C
attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets methods
[8] base
other attached packages:
[1] edgeR_3.2.3          Biobase_2.20.0       BiocGenerics_0.6.0
[4] limma_3.16.5         BiocInstaller_1.10.1 RColorBrewer_1.0-5
loaded via a namespace (and not attached):
[1] tools_3.0.1

-- 
Julien Roux, PhD
Gilad lab, Department of Human Genetics, University of Chicago
http://giladlab.uchicago.edu/
920 East 58th Street, CLSC 317, Chicago, IL 60637, USA
tel: +1-773-834-1984   fax: +1-773-834-8470


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