I think it could be an Excel interpreation of '-Inf' ? just my guess.. Alessandro ----------------------------------------------------- Alessandro Guffanti - Bioinformatics, Genomnia srl Via Nerviano, 31 - 20020 Lainate, Milano, Italy Ph: +39-0293305.702 Fax: +39-0293305.777 http://www.genomnia.com "If you can dream it, you can do it" (Walt Disney) -----Original Message----- From: Gordon K Smyth <smyth@wehi.edu.au> To: Jared Bischof <jared@alum.northwestern.edu> Cc: Bioconductor mailing list <bioconductor@r-project.org> Date: Sun, 29 Apr 2012 11:20:55 +1000 (AUS Eastern Standard Time) Subject: [BioC] NaN p-values from edgeR 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/ [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@alum.northwestern.edu> > To: <bioconductor@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 > ______________________________________________________________________ The information in this email is confidential and inten...{{dropped:28}}

Thanks Gordon. I'm not sure what was causing that output but updating to the newest version of edgeR fixed the problem. Thanks, Jared On Sat, Apr 28, 2012 at 8:20 PM, Gordon K Smyth <smyth at="" wehi.edu.au=""> wrote: > 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 >> > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:6}}