[BioC] Bioconductor Digest, Vol 116, Issue 8

Thomas J Hardcastle tjh48 at cam.ac.uk
Mon Oct 8 12:52:06 CEST 2012

A sample size of 10000 is usually sufficient, unless your data are 
particularly unusual. For maximum stability and accuracy of prior 
distribution estimation, you can use 24000 (i.e., every data point) - 
this will take slightly longer to run but may give very slight improvements.

Best wishes,


On 08/10/12 11:00, bioconductor-request at r-project.org wrote:
> ------------------------------
> Message: 8
> Date: Mon, 08 Oct 2012 09:50:48 +0000
> From: Fatemehsadat Seyednasrollah<fatsey at utu.fi>
> To:"bioconductor at r-project.org"  <bioconductor at r-project.org>
> Subject: [BioC] baySeq and samplesize factor
> Message-ID:
> 	<26055A619290434EA444B0C7E5DEFAF4538EFB3C at exch-mbx-01.utu.fi>
> Content-Type: text/plain; charset=us-ascii
> Hi all,
> I need to do some RNA seq analysis in order to get DE genes. I want to use baySeq from Bioconductor but as the estimation should be very accurate I wanted to know what is the best "samplesize" amount for function "getPriors.NB" if my dataset has 24000 rows.
> Many thanks in advance.
> ------------------------------

Dr. Thomas J. Hardcastle

Department of Plant Sciences
University of Cambridge
Downing Street
Cambridge, CB2 3EA
United Kingdom

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