[BioC] LIMMA: How do I get the standard deviation?

Sebastian Thieme Tobar at gmx.de
Fri Feb 4 00:21:04 CET 2005


Hello !

To get the intensities of R and G channel I use RG.MA() on normalized data 
set.
I can calculate the standard deviation using simple function sd( ). But 
there  the spot duplicates are not taken into account, only slide replicates.
After running lmFit(), eBayes() and topTable() the duplicates are accounted.
But how can I get from that results the standard deviation?
Does it correspond to $stdev.unscaled from lmFit() output and can I use 
that for simple graphics (like R to G channel with sd-bars)?

Thanks !

Sebastian Thieme



More information about the Bioconductor mailing list