Entering edit mode
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
>