[BioC] Fwd: edgeR with only 1 replicate?

Jenny Drnevich 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
>330 ERML
>1201 W. Gregory Dr.
>Urbana, IL 61801
>ph: 217-244-7355
>fax: 217-265-5066
>e-mail: drnevich at illinois.edu

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