[BioC] qvalue pi0 computation

[naomi at stat.psu.edu]

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
>