Hi,
I had a related question regarding BCV, it has been my recent experience
that working in vivo with heterogeneous tissues such as brain yields a much
higher BCV than 10%, usually close to 30%
even though I am working with genetically identical organisms (mice, all
males as well).
Is that your observation as well, or does this mean that variation is being
introduced at some of the sample processing steps?
I do not have technical replicates, although I have n=5 biological
replicates for each of my conditions
Interestingly, filtering out low count reads does not seem to lower the
average BCV much

thanks very much for your answer

Lucia


On Fri, Aug 10, 2012 at 9:40 PM, Gordon K Smyth <smyth@wehi.edu.au> wrote:

> See fourth paragraph of the Discussion of the edgeR glm paper:
>
> http://nar.oxfordjournals.org/**content/40/10/4288.long<http://nar.oxfordjournals.org/content/40/10/4288.long>
>
> Gordon
>
>  Date: Fri, 10 Aug 2012 11:45:31 +0300
>> From: KJ Lim <jinkeanlim@gmail.com>
>> To: Bioconductor mailing list <bioconductor@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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