Hi Guys,


while i run DESeq, I have got some questions.

It looks like there is no way to handle genes with zero read counts in DESeq
as the returned values are all NA for below two cases
               1. totally no information for two groups as like 0 0
               2. uniquely expressed genes as like 0 c(constant) or c 0

In DESeq, when M-D plot is generated or de analysis is performed, it looks
like those genes in M-D plot are all discarded and DESeq returns just NA
values for such cases. is that correct?

if yes, for genes with uniquely expressed genes, it could be informative.
isn't it?  to my knowledge, DEGseq and edgeR they are doing a simple way for
such cases. so, there is no NA value in the output even there are genes with
zero read counts as the input.

Could you please explain how to handle genes with zero read counts in DESeq
package?


Thanks in advance, --S

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