Thanks Naomi, This is what I have been doing, but as I said, this is very laborious (especially when you have 50-200 arrays per project). I was hoping within limma there was an easy way of doing this, it seems like a very straightforward thing to implement, and a dedicated command for averaging reps would be very helpful to a lot of people. Subsetting and doing this manually, discourages use of limma, given the laborious nature of the process. Thanks Simon.

You might consider implementing this yourself and then contributing a patch. I can't speak for Gordon, but in general, open source developers are quite receptive to contributions from end users. Best, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Simon Melov <smelov@buckinstitute.org> 05/19/04 12:40PM >>> Thanks Naomi, This is what I have been doing, but as I said, this is very laborious (especially when you have 50-200 arrays per project). I was hoping within limma there was an easy way of doing this, it seems like a very straightforward thing to implement, and a dedicated command for averaging reps would be very helpful to a lot of people. Subsetting and doing this manually, discourages use of limma, given the laborious nature of the process. Thanks Simon. _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor