[BioC] problem normalizeMedians (limma)

Francois Pepin fpepin at cs.mcgill.ca
Tue Oct 18 00:24:47 CEST 2005

Hi everyone,

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$A[1,1]
[1] 8.796361
> dat <- normalizeBetweenArrays(dat)
> dat$A[1,1]
[1] Inf

This is due to the fact that I've got almost 400 arrays here. The
normalizeMedians(x) (which is called by normalizeBetweenArrays) has the
following behavior:

    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.

> 6^400 
[1] Inf

Wouldn't it be better to be working in log space instead?


> sessionInfo()
R version 2.1.0, 2005-04-18, x86_64-unknown-linux-gnu

attached base packages:
[1] "methods"   "stats"     "graphics"  "grDevices" "utils"
[7] "base"

other attached packages:

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