[BioC] EdgeR: artifacts on BCV plot

[Gordon K Smyth]

Hi Ryan,

It is not possible for the dispersion to be less than zero in a negative 
binomial distribution (because the distribution would become 
mathematically undefined).  Hence it is not possible for edgeR to estimate 
a negative dispersion value, and there is no need to do any correction.

You might be thinking of other packages that use moment estimation or 
other ad hoc means to estimate the dispersion.  edgeR is a 
likelihood-based package, so the restriction to valid parameter values is 
inherent in the algorithm.

Gordon

On Sat, 1 Feb 2014, Ryan wrote:

> Hi Gordon,
>
> Does edgeR always force dispersion values to be non-negative? In other words, 
> if the edgeR estimates a negative dispersion value for a given gene, does it 
> simply replace that dispersion with zero?
>
> -Ryan
>
> On Sat Feb  1 17:35:28 2014, Gordon K Smyth wrote:
>>> 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
>> 
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