[BioC] medain global normalize - argument matrix
Gordon K Smyth
smyth at wehi.EDU.AU
Tue Nov 6 08:33:45 CET 2012
Dear MAB,
normalizeMedianValues() in the limma package does exactly this.
Best wishes
Gordon
------------ original message ----------------------
[BioC] medain global normalize - argument matrix
Mark B mablfm at gmail.com
Sat Oct 27 23:13:51 CEST 2012
Hi,
I am trying to normalize a matrix of logged (base 2) cDNA expression
intensity values (dimensions 4000, 4) from only the Cy5 channel derived
from an marrayraw object. I would like to normalize the values
using global median normalization where all arrays result having the same
median value. I would also like a matrix returned from the function.
I have found how to use this normalize using an marrayraw object as
argument ( e.g. maNorm(m, norm="median") ) but I can't seem to find how to
do this with a matrix as argument.
I have also tried the following but while my argument is a matrix my
output is a numeric vector that I can't seem to coerce back into a matrix
with the same dimensions I started with.
# median normalize all samples (columns)
s.median <- apply(s, 2, median)
class(s.median)
[1] "numeric"
Any hints?
Thanks in advance,
MAB
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