Question: Should zero expression ever be tested for significance?
0
gravatar for ivan.o.kryukov
3.5 years ago by
Canada
ivan.o.kryukov0 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?

 

 

rna-seq • 927 views
ADD COMMENTlink written 3.5 years ago by ivan.o.kryukov0
1
imagine that the most highly expressed gene in condition A is switched off completely in condition B and has therefore 0 counts. wouldn't you think that's a very significant difference? that said, I don't know exactly the steps in cuffdiff
ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by Martombo2.4k

This 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.

ADD REPLYlink written 3.5 years ago by ivan.o.kryukov0
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