[BioC] Fwd: edgeR with only 1 replicate?
drnevich at illinois.edu
Thu Jul 23 18:02:12 CEST 2009
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.
>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
>1201 W. Gregory Dr.
>Urbana, IL 61801
>e-mail: drnevich at illinois.edu
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