[BioC] NaN p-values from edgeR

[Gordon K Smyth]

Dear Jared,

edgeR does not generate NaN p-values as far as I know so, no, we have not 
seen this before.

Your output shows that you are not using the current release version of 
edgeR.  Please try installing the current version.

As Wolfgang said in his reply, we like to see sessionInfo() and more 
information about how output was generated.  Making useful comments on 
snippets of output is hard.  Have a look at the posting guide:

http://www.bioconductor.org/help/mailing-list/posting-guide/

Best wishes
Gordon

> Date: Fri, 27 Apr 2012 14:00:29 -0500
> From: Jared Bischof <jared at alum.northwestern.edu>
> To: <bioconductor at stat.math.ethz.ch>
> Subject: [BioC] NaN p-values from edgeR
>
> 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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