[BioC] EdgeR: artifacts on BCV plot

[Ryan]

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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