[BioC] RMA median polish to a matrix

[Ben Bolstad]

You could use preprocessCore:

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

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
estimates.

Best,

Ben

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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