[BioC] EdgeR: artifacts on BCV plot

[Gordon K Smyth]

> Date: Fri, 31 Jan 2014 11:59:13 +0000
> From: Adriaan Sticker <adriaan.sticker at gmail.com>
> To: Ryan <rct at thompsonclan.org>
> Cc: bioconductor at r-project.org
> Subject: Re: [BioC] EdgeR: artifacts on BCV plot
>
> Hi
> Thanks for your input. I checked manually the counts of the lowest BCV
> values (see below) And I see nothing strange. Except the fact that the
> counts are all at the low side. So I think I will keep them in.
> Is it correct to think that the reason they appear on 1 horizontal line is
> because of the discreteness of the counts?

No it is not because of discreteness.  It is because zero is 
mathematically a perfectly possible value for the BCV.

These genes appear to show variability that is equal or less than Poisson 
variability, even after pulling them up towards the dispersion trend.  In 
other words, these genes are not showing any evidence of differences 
between biological replicates.

Gordon

> Greetings
> Adriaan

______________________________________________________________________
The information in this email is confidential and intend...{{dropped:4}}