You can use limma, multtest, siggenes, or factDesign (if you have a factorial experiment). Which package to use is partially dependent on your experimental design, so I would recommend looking at the help for each one to see which fits best. 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 >>> "Fan, Wenhong" <wfan@fhcrc.org> 04/30/04 7:20 PM >>> Dear all, In Bioconductor, I use affy package to extract the gene expression from Affy chips. Then I need to do the downstream analysis of differentially expressed genes. What are available to do this in Bioconductor? Best regards, Wenhong ****************************************************************** Fred Hutchinson Cancer Research Center M2-B500 1100 Fairview Ave. North Seattle, WA 98109 (206) 667-7256 _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor