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

[KJ Lim]

Dear Prof Gordon,

Thanks for your prompt replied. I will read through the paper.

Have a nice weekend.

Best regards,
KJ Lim


On 11 August 2012 04:40, Gordon K Smyth <smyth at wehi.edu.au> wrote:
> See fourth paragraph of the Discussion of the edgeR glm paper:
>
> http://nar.oxfordjournals.org/content/40/10/4288.long
>
> Gordon
>
>> 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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