[BioC] edgeR: Value of variation of biological variation (BCV)

Gordon K Smyth smyth at wehi.EDU.AU
Sat Aug 11 03:40:58 CEST 2012

See fourth paragraph of the Discussion of the edgeR glm paper:



> Date: Fri, 10 Aug 2012 11:45:31 +0300
> From: KJ Lim <jinkeanlim at gmail.com>
> To: Bioconductor mailing list <bioconductor at r-project.org>
> Subject: [BioC] edgeR: Value of variation of biological variation (BCV)
> Dear edgeR users and R community,
> I'm analysing a set of RNA-Seq data which has 2 different genotypes
> (treeHS, treeLS) and time of treatment (0H, 3H, 24H, 96H) with edgeR.
> After carried out estimating the common dispersion, the value of BCV
> for my RNA-Seq data was 0.428.
>  > hl <- estimateGLMCommonDisp(hl, hl.design, verbose=TRUE)
>  Disp = 0.18319 , BCV = 0.428
> May I ask, it is common to see the value of variation of biological
> variation (BCV) as such? What this value can tells about the RNA-Seq
> data? I have these thoughts wondering me for a while. Forgive me if I
> have asked a stupid question.
> Thank you very much for your time.
> Have a nice weekend.
> Best regards,
> KJ Lim

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