Hi,
I am trying to normalize a matrix of logged (base 2) cDNA expression
intensity values (dimensions  4000, 4) from only the Cy5 channel derrived
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

	[[alternative HTML version deleted]]

