Hello,

The CuffDiff tool at the main/test public instances and in the last dist should all support multiple groups. If you want detailed help for the Cuff* tools, then the tool author's support list might be able to help: tophat.cuffli...@gmail.com.


Best wishes for your project,

Jen
Galaxy team

On 10/1/11 5:57 AM, An, Hongyan wrote:
I have 3 groups of accepted hits, each group has 3 replicates. When I add 3 
groups with corresponding replicates, the cuffdiff output only gave 2 groups 
comparison of differential expression, Please help me here

------
Hongyan An, Ph.D.
Research Associate
Genomics Core of Yale Stem Cell Center
Yale University School of Medicine
10 Amistad Street Room 203
New Haven, CT 06520
phone: (203)-737-6203
Fax: (203) 785-4305
hongyan...@yale.edu<mailto:hongyan...@yale.edu>

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