Hi Everyone,
I have been using edgeR for the last couple years with great success.
Thanks very much. Now I have slightly unconventional dataset to try. We
have two groups to compare (life stages) each with three replicates. But,
for each sample in each group, we made two different RNAseq libraries.
1)   one from fragmented mRNA (classical RNAseq) and
 2)  another from Ribosome-bound RNA fragments. This library would indicate
how much of the RNA is actively being translated.

I have used edgeR to analyse data from each of this separately (data from
classical RNAseq or Ribosome-bound). So this let us study the
differentially transcribed genes or differentially translated genes.  And
got really nice results.

The next step is to compare the translational efficiencies between them. In
each sample the ratio between read counts of Ribosome bound mRNAs and
fragmented mRNA would give us the translational efficience of that gene. We
can generate these efficiences (ratios) for each of the three replicates in
each group. Can I feed this data to edgeR to find out which genes have
'differential efficiencies'  between groups?

I understand, edgeR insists on NOT normalizing the read counts and all the
further statistics depends on the total library size count. By, using
ratios, i completely throw edgeR off. But, i am not sure what is the best
alternate to this?

Any ideas?

Much thanks in advance,
Gowthaman


-- 
Gowthaman

Bioinformatics Systems Programmer.
SBRI, 307 West lake Ave N Suite 500
Seattle, WA. 98109-5219
Phone : LAB 206-256-7188 (direct).

	[[alternative HTML version deleted]]

