[BioC] qvalue pi0 computation
James W. MacDonald
jmacdon at uw.edu
Tue Feb 19 22:06:37 CET 2013
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
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: 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
More information about the Bioconductor
mailing list