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=""> escribi?: > 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). >> > > ______________________________________________________________________ > The information in this email is confidential and intend...{{dropped:4}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor