[BioC] qvalue pi0 computation

[James W. MacDonald]

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 at 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 at 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