Hi, I have analyzed my chip data using the rma function. After rma computations I examined the distribution of intensities over the chips. As the rma function employs the quantile normalization I expected to get identical distribution for all the chips. The distributions that I get are similar but not identical. Why is it so? Have I missed something? I would really appreciate your help. -Rani. [[alternative HTML version deleted]]

because its the probe intensities that are quantile normalized not the expression values. On Wed, 21 Jan 2004, Rani Elkon wrote: > Hi, > > I have analyzed my chip data using the rma function. After rma computations I examined the distribution of intensities over the chips. As the rma function employs the quantile normalization I expected to get identical distribution for all the chips. The distributions that I get are similar but not identical. Why is it so? Have I missed something? > > I would really appreciate your help. > > -Rani. > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >