I am analyzing microbiome data from human gut samples and wanted to do DESeq2 analysis. I have lots of
NAs in my count matrix. The reason I have NA's is because one sample may have a particular group of microorganisms that is completely or partially present in other samples.
Normally, I don't get NAs while analyzing RNAseq data from a species, but for this microbiome I am getting lots of NAs. How should I deal with these NAs? Should I remove the rows with one or more NAs from the count matrix or replace NAs with zero(as they may not be part of that sample's microbiome). If I remove rows with NAs, I will be left with only 5 rows (very few loci are shared across all samples). Any suggestion would be appreciated. Thanks