[BioC] Fwd: edgeR with only 1 replicate?

[Mark Robinson]

Hi Jenny.

You won't be able to estimate the negative binomial dispersion  
parameter without replication.  In edgeR, you can set doPoisson=TRUE  
in deDGE() which basically just sets that parameter to 0.  I think  
this comes out quite similar to sage.test().

Cheers,
Mark

On 24/07/2009, at 5:41 AM, Naomi Altman wrote:

> I used sage.test for NGS libraries.  Worked fine.
> --Naomi
>
> 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.
>>>
>>> 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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>
> Naomi S. Altman                                814-865-3791 (voice)
> Associate Professor
> Dept. of Statistics                              814-863-7114 (fax)
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------------------------------
Mark Robinson, PhD (Melb)
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robinson at garvan.org.au
e: mrobinson at wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852