One point that may be relevant is that qvalue has multiple distribution points. You may have been using http://genomics.princeton.edu/storeylab/qvalue/qvalue_1.1.tar.gz (described as the linux or mac distribution) or any of the versions at http://cran.r-project.org/src/contrib/Archive/qvalue/ On Tue, Feb 19, 2013 at 4:06 PM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Naomi, > > The qvalue package hasn't been updated in years. The last two changes were > by Patrick Aboyoun and Robert Gentleman, and those were changes that are > highly unlikely to affect the qvalue() function itself: > > [jmacdon@adam2 R]$ svn log -v -r {2013-02-19}:{2007-01-01} > ------------------------------**------------------------------** > ------------ > r46457 | p.aboyoun | 2010-04-23 00:32:56 -0700 (Fri, 23 Apr 2010) | 1 line > Changed paths: > M /trunk/madman/Rpacks/qvalue/**DESCRIPTION > A /trunk/madman/Rpacks/qvalue/**NAMESPACE > M /trunk/madman/Rpacks/qvalue/R/**qvalue.R > > Added NAMESPACE file and removed unneeded .First.lib function. > ------------------------------**------------------------------** > ------------ > r27129 | rgentlem | 2007-09-13 22:46:43 -0700 (Thu, 13 Sep 2007) | 2 lines > Changed paths: > M /trunk/madman/Rpacks/qvalue/**DESCRIPTION > M /trunk/madman/Rpacks/qvalue/R/**qvalue.R > > fixed up a missing tcltk dependency > > ------------------------------**------------- > > So those are two ancillary changes since 2007! I would venture a guess > that the differences are not due to changes to the qvalue package itself. > > The package imports some functions from the stats package: > > importFrom(stats, predict, quantile, smooth.spline) > > But again, I would be surprised if there were fundamental changes to any > of those functions. Changing how predict() or quantile() work would spark > an insurrection that I am sure we would have heard about. > > Best, > > Jim > > > > > On 2/19/2013 3:51 PM, naomi@stat.psu.edu wrote: > >> I just updated R and Bioconductor and reran an analysis. In particular >> >> qvalue(p)$pi0 >> >> is giving me really different answers than the last time I ran it (same p) >> about a year ago. >> >> Any hints as to why would be most appreciated. Session info is below for >> the current session. I do not have the information for a year ago. >> >> --Naomi >> >> >> >> sessionInfo() >>> >> R version 2.15.2 (2012-10-26) >> Platform: x86_64-w64-mingw32/x64 (64-bit) >> >> locale: >> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >> States.1252 >> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C >> [5] LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] qvalue_1.32.0 maanova_1.28.0 limma_3.14.4 >> >> loaded via a namespace (and not attached): >> [1] Biobase_2.18.0 BiocGenerics_0.4.0 grid_2.15.2 >> lattice_0.20-13 >> [5] nlme_3.1-108 tcltk_2.15.2 tools_2.15.2 >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > [[alternative HTML version deleted]]