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!