I want to use edgeR to look at differential gene expression. I have a metatranscriptome m= 1 221 663 ORFs and n= 83 samples with (m= 34 control, and m= 49 experimental) samples. I can trim out many of these ORFs if necessary to include only ORFs that have hits in at least 75% of the samples m = 101 010 ORFs.
My questions are:
(1) Can edgeR be used for metatranscriptomic analysis? i.e. Can the assumptions of the model be applied to multiple organisms in a community?
(2) If I have a subset of genes (e.g. the 101 010 ORFs from the 1 221 663 total ORFs) and run edgeR's exactTest, will I get the same results for those ORFs if I ran them with the entire 1 221 663 ORFs set?
(Bonus) Are there any tools that are better for this? I saw metagenomeSeq but I think that is more for 16S amplicon work.
