Hi Michael,

I have a count matrix with quite a few of missing values, and these missing values are not allowed in DESeq2.

What is the best way to deal with them?

If all missing value are set as 0, how much it affect the differential expression analysis results?

Thank you!

The first question is why you have missing data. I don't know of a method to generate counts/gene that results in NA values (zeros, sure, but NA?).