[BioC] RMA median polish to a matrix

Ben Bolstad bmb at bmbolstad.com
Thu Jan 24 16:23:03 CET 2008

You could use preprocessCore:

x <- outer(c(seq(-2,2,0.4)),c(8:12),"+") + rnorm(55)

with the first A values of the return value item $Estimates giving the
gene expression values

Alternatively, if you want to use medpolish(), take the 

"Column Effects" and add the "Overall" to get the gene expression



On Thu, 2008-01-24 at 15:53 +0100, Naira Naouar wrote:
> Dear all,
> I have a matrix of intensities for one gene: PxA where P represents the 
> number of probes and A the number of arrays; and I would like to summarize 
> the probe intensities values in order to get 1 value/ array for this gene 
> using the median polish algorithm.
> The medpolish fonction in R provides me the overall median and the 
> residuals terms relative to the additive model behind the median polish 
> but I am not quite sure on how to add this values to get the correct 
> expression value for the gene for each array.
> Thanks a lot for your help,
> Naira
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