Hi, I have a question about the output of se.exprs. I normalized a data set using expresso and the model from Irizarry et al (2003) Biostatistics paper. rma.dta<-expresso(raw.data, normalize.method="quantiles.robust", bkground.correct="rma", summary.method="medianpolish", pmcorrect.method="pmonly") I can extract the expression values using exprs.rma<-exprs(rma.dta) and could compute a sample standard deviation from se.rma<-sqrt(apply(exprs.rma, 1, var)). The square of this estimates the variance of the individual expression values. I can also extract the model-based estimate of the standard deviation from se.model.rma<-se.exprs(rma.dta) I'm not sure whether se.model.rma (squared) estimates the variance of the individual espression values. For further clarification and statistical notation pls see the attached pdf file. This question was motivated by my observation that the sample standard deviation is substantially larger than the model-based standard deviation in a dataset that I am working with. Many thanks in advance, Mary Puttse. exprs.pdf -------------- next part -------------- A non-text attachment was scrubbed... Name: se.exprs.pdf Type: application/pdf Size: 44433 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20030702/d0caedbd/se.exprs-0001.pdf