[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
More information about the Bioconductor
mailing list