[BioC] adj.P metod = \"BH\" many exact the same value
Bas ter Braak [guest]
guest at bioconductor.org
Thu Apr 4 11:51:53 CEST 2013
Dear list,
I was converting the p values of my DEG list to adjusted p-values (using benjamin Hochberg) and found out that many adjusted p-values have the exact same value. (using topTable from limma package)
Is this normal and what is the reason for this observation?
thanks in advance,
cheers,
Bas
-- output of sessionInfo():
R version 2.15.3 (2013-03-01)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] limma_3.14.4 affy_1.36.1 Biobase_2.18.0 BiocGenerics_0.4.0
loaded via a namespace (and not attached):
[1] affyio_1.26.0 BiocInstaller_1.8.3 preprocessCore_1.20.0 tools_2.15.3 zlibbioc_1.4.0
--
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