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Do counts need to be filtered for edgeR to properly work on metatranscriptome?

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.

rna-seq metagenomics metatranscriptomics edger
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written by O.rka O.rka

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