[BioC] NaN p-values from edgeR

[Wolfgang Huber]

Dear Jared

I have no substantial input here, but I expect it would be helpful if 
you supplied the exact script you ran and the output of sessionInfo().

	Best wishes
	Wolfgang


Apr/27/12 9:00 PM, Jared Bischof scripsit::
> Hi all, I'm a computational biologist at Children's Memorial Hospital
> in Chicago.  I'm using the edgeR library to compare RNA-seq datasets.
> But, recently I was running a comparison and got an error that led me
> to the realization that some of the p-values were being returned as
> "NaN".  I searched the message archives and found messages addressing
> the Fold Change sometimes showing up as NaN but this is the p-values
> in my case.  I checked the input and neither of the tag counts is zero
> so I know that's not part of the issue.  Has anyone seen this before?
> I'm wondering what this represents in this case.  I thought that
> perhaps this represented a p-value of essentially zero but looking at
> the input data that is clearly not the case.  Here's part of the
> counts table:
>
>           Tumor3TagCounts Tumor5TagCounts
> FR138965          171971           27074
> FR077061          155101           39388
> FR273624          153178           38882
> FR121537          100582           83496
>
> And here's a relevant section of the table from the exactTest output:
>
>             logConc      logFC      p.value
> FR138965 -4.621888 -0.5596774 0.000000e+00
> FR077061 -4.425942  0.1301280 1.534497e-50
> FR273624 -4.444269  0.1294732 1.923549e-49
> FR121537 -4.196385  1.8389148          NaN
>
> I can't reason that NaN represents a p-value of zero because the
> transcript FR273624 has an even greater difference and does not return
> a p-value of zero.
>
> Thanks in advance,
> Jared Bischof
>
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-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber