[BioC] medain global normalize - argument matrix

[Gordon K Smyth]

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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