[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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