Hi, I am using the oligo package for ST gene arrays, and I have some questions about the MAplot() function in the oligo package. This is part of my sessionInfo(): > sessionInfo() R version 2.15.2 (2012-10-26) Platform: i386-w64-mingw32/i386 (32-bit) other attached packages: [1] pd.hugene.1.0.st.v1_3.8.0 RSQLite_0.11.2 [3] DBI_0.2-5 oligo_1.22.0 [5] Biobase_2.18.0 oligoClasses_1.20.0 [7] BiocGenerics_0.4.0 And this is the MAplots that I tried to generate: > myData <- read.celfiles(celFiles) > MAplot(myData, ylim=c(-2, 2)) > eset <- rma(myData, target="core") > MAplot(myData, ylim=c(-2, 2)) So I have two sets for MA plots one for the raw CEL file values and one for the RMA normalized values. My questions are: 1. About the median and IQR values reported on each plots, are they for the M values? 2. In the MA plots for the RMA values, should the loess line be very close to the horizontal 0 line? What does it mean if it's not? 3. My MAplots for the RMA values all have median and IQR values of 0. I understand that the median should be 0, but how about IQR? Should that all be 0 as well? If one array is not, is that an outlier? Thank you very much for your help! Yiwen CIT/NIH/HHS