[BioC] problem normalizeMedians (limma)
fpepin at cs.mcgill.ca
Tue Oct 18 00:24:47 CEST 2005
I'm not sure what should be done about it, but I've been surprised with
the following behavior with normalizeBetweenArrays:
(dat is an MAList here)
> dat <- normalizeBetweenArrays(dat)
This is due to the fact that I've got almost 400 arrays here. The
normalizeMedians(x) (which is called by normalizeBetweenArrays) has the
a.med <- apply(x, 2, median, na.rm = TRUE)
a.med <- a.med/(prod(a.med))^(1/narrays)
multiplying 400 relatively small numbers can easily reach R's limit as
far as doubles are concerned.
Wouldn't it be better to be working in log space instead?
R version 2.1.0, 2005-04-18, x86_64-unknown-linux-gnu
attached base packages:
 "methods" "stats" "graphics" "grDevices" "utils"
other attached packages:
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