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
>> ______________________________**_________________
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>>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>
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