Maximum Number of Gene in a DESeq2 and edgeR

Question

[rieza.aprianto]

Hey all,

I am planning a metagenomic differential gene analysis of samples in two conditions, each with two replicates. My question is what is maximum number of genes that we can enter into a DESeq2 or EdgeR models to get a statistically sound differential expression analysis.

Background: the samples contains many species of bacteria, and I am worry that DEG Analysis can not give meaningful results because there are an upper limit of number of genes I can funnel into the model.

Thanks in advance!

Answer 1

[Carlo Yague]

Hi !

Although I might be wrong, I don't think there is an upper limit to the number of genes to test. Instead, in DESeq2 (perhaps in EdgeR too), the variation of a gene expression (they call it "dispersion") is estimated from its individual variation but also from the variation of genes with similar expression level (mean of normalized counts). So the more genes you have, the more accurate this estimation will be.