Question: Should zero expression ever be tested for significance?

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ivan.o.kryukov •

**0**wrote: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?

2.4kThis makes sense biologically, yes. But I am not sure what statistical basis there could be for comparing 0s (other than pseudocounts, or Bayesian priors). In the previous cases I've seen - those are not compared at all. Otherwise, they will automatically _always_ given you a significant difference.

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