[BioC] edgeR: Using ratios (translational efficiencies) as input

[Wolfgang Huber]

Gowthaman

as far as I understand, your library 2 falls in the class of 'iCLIP' experiments.
Perhaps the methods part of this paper can provide some analysis ideas: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3629564/

I believe that the 'offset' matrix in edgeR or the 'per-gene normalisation factors' of DESeq2 could also be useful in this context.

	Best wishes
	Wolfgang

El Apr 29, 2013, a las 8:37 am, Gordon K Smyth <smyth at wehi.edu.au> escribió:

> Dear Gowthaman,
> 
> I'm not quite sure what translational efficiencies are.  Do you have a different efficiency value for each gene and each RNA sample?  If you do, why not take logs of the ratios (offsetting counts by 1/2 or 1 to avoid zeros) and feed them into limma?
> 
> Best wishes
> Gordon
> 
>> Date: Fri, 26 Apr 2013 15:22:28 -0700
>> From: gowtham <ragowthaman at gmail.com>
>> To: bioconductor <Bioconductor at r-project.org>
>> Subject: [BioC] edgeR: Using ratios (translational efficiencies) as
>> 	input
>> 
>> 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).
>> 
> 
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