The help for plotMA (found by typing ?plotMA at an R prompt with the limma package loaded) says the following: Arguments: MA: an 'RGList', 'MAList' or 'MArrayLM' object, or any list with components 'M' containing log-ratios and 'A' containing average intensities array: integer giving the array to be plotted. Corresponds to columns of 'M' and 'A'. So it looks like you need to set array = 2, etc to do the other MA plots. HTH, 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 >>> Hao Liu <liuha@umdnj.edu> 07/23/04 04:32PM >>> Dear all: I read 12 cDNA experimental data into RGwt, when I use plotMA, only 1 shows up, how do I show others? I can't find documentation for it anywhere. Thanks Hao Liu, Ph. D _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor