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

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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Hi all, I just discovered the medianpolish function which does exactly what I need :) Cheers, Naira On Thu, 24 Jan 2008, 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >