[BioC] downstream analysis of differentially expressed genes

James MacDonald jmacdon at med.umich.edu
Sat May 1 01:41:35 CEST 2004

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.



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
>>> "Fan, Wenhong" <wfan at 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,


Fred Hutchinson Cancer Research Center
1100 Fairview Ave. North
Seattle, WA 98109
(206) 667-7256

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