You should probably use expresso, justRMA or gcrma to normalize these data. You should be using the "affy" library, not the marray library. If you really prefer loess and if the arrays are paired with one treatment and one control in each rep you can do the following: M= log(trt)-log(ctrl) A=(log(trt)+log(ctrl))/2 loess.out=loess(M~A) norm.data=loess.out$residual You will get one normalized value for each gene for each rep. To get more help on loess, just type "?loess", as I have not given you all the options. --Naomi At 04:07 PM 4/30/2004, E Motakis, Mathematics wrote: >Hi, >I am a rather new user of Bioconductor and I have one question. Which >function should I use to "loess" normalize gene intensities from an >experiment conducted with AFFYMETRIX? The experiment contains 3 replicates >with one treatment and one control condition for the genes. >I cannot understand how I should use function "read.marrayRaw" if this is >the correct one. > >Thanks in advance. > >Makis > >---------------------- >E Motakis, Mathematics >E.Motakis@bristol.ac.uk > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Naomi S. Altman 814-865-3791 (voice) Associate Professor Bioinformatics Consulting Center Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111