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

[Kasper Daniel Hansen]

On Wed, Aug 3, 2011 at 7:09 PM, Davis McCarthy <dmccarthy at wehi.edu.au> wrote:

> We have used this gene-specific normalization factor to try out things like quantile normalization on RNA-Seq data in house. To my knowledge, the new cqn package outputs gene-specific offsets that will plug in to edgeR to normalize data for (possibly among other things) gene length and GC bias.

True, but the interface to the cqn normalization method assumes that
the data is ordered in a "genes" by samples matrix and that all
samples have the same length/gc content for a given gene.  The data we
are discussing does not fit into this framework.  However, it might be
possible to hack the function to deal with this, by running
  cqn(..., sqn = FALSE)
on each species separately, combining the output and then do a custom
sqn normalization of the combined residuals.  Hmm, this clearly
requires more than 60 secs. of thinking (and probably some careful
looking at the output to get an idea of whether this gives useful
output or makes things worse).

Kasper