[BioC] NaN p-values from edgeR

Jared Bischof jared at alum.northwestern.edu
Fri Apr 27 21:00:29 CEST 2012


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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