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]]