Question: Fwd: edgeR with only 1 replicate?
10.0 years ago by
Jenny Drnevich • 1.9k
Jenny Drnevich • 1.9k wrote:
Forgot to Cc: BioC the first time... >Date: Thu, 23 Jul 2009 10:23:11 -0500 >To: "Mark Robinson" <mrobinson at="" wehi.edu.au=""> >From: Jenny Drnevich <drnevich at="" illinois.edu=""> >Subject: edgeR with only 1 replicate? > >Hi Mark and others, > >Can edgeR be used if you only have 1 replicate per group? If not, do >you or anyone know of the best way to analyze frequencies of >Illumina's DGE tags. I'm thinking Fisher's exact test or Z-test, but >it would be nice if the functions for sequencing data were already >written. I see from searching the BioC archives that there is >sage.test, which is Fisher's exact test - anything else? Most of the >work done on this has been in the context of SAGE libraries, and I >wonder if it scales properly to NGS libraries. > >Thanks, >Jenny > >Jenny Drnevich, Ph.D. > >Functional Genomics Bioinformatics Specialist >W.M. Keck Center for Comparative and Functional Genomics >Roy J. Carver Biotechnology Center >University of Illinois, Urbana-Champaign > >330 ERML >1201 W. Gregory Dr. >Urbana, IL 61801 >USA > >ph: 217-244-7355 >fax: 217-265-5066 >e-mail: drnevich at illinois.edu
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