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

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