[BioC] Fwd: edgeR with only 1 replicate?

Naomi Altman naomi at stat.psu.edu
Thu Jul 23 21:41:31 CEST 2009

I used sage.test for NGS libraries.  Worked fine.

At 12:02 PM 7/23/2009, Jenny Drnevich 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.
>>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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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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