I am trying to figure out when the comparison between FPKM is performed in `cuffdiff`. The `NOTEST` clause is invoked when both values are close. If one of the values is zero, there should be no testing for significance (or so it seems). However, using version `2.2.1`, I get several examples where `-inf` log fold change results in a significant q-value (always 0.047).
I have checked, and for all of such cases, I get no reads for the transcripts in question.
#regular case - no objections here
OK 2.7692 0 -inf -nan 0.0011 0.226273
#weird case - not sure why this is "significant"
OK 2.71508 0 -inf -nan 5e-05 0.0470179 yes
Is there a general case where 0 expression is tested?