[BioC] EdgeR: artifacts on BCV plot

[Gordon K Smyth]

Dear Adriann,

On Sun, 2 Feb 2014, Adriaan Sticker wrote:

> Dear Gordon,
>
> Thanks a lot for your input. I tried the automatic prior.df estimation of
> the estimateDisp() function. and its suggests a much lower prior.df then I
> put mannually (9 instead of 25) But when I look at the gof plot, it's way
> off. I thought that a good guide for a prior.df estimation is looking for a
> value that puts the calculated deviances as close as possible to the
> theoretical espected values. This is the prior.df for which your deviances
> are straight on the  diagonal line of gof / qq plot)

Not this isn't so.  The value returned by estimateDisp() is better.

Plotting the gof is valid for showing that the common or trended 
dispersion models are inadequate, but the QQ plot of the GOF statistics 
doesn't work properly any more once the tagwise dispersions have been 
estimated.  This is because the tagwise dispersions are estimated from the 
same genewise data that is being plotted.

I admit that we have not made that sufficiently clear in the 
documentation.

Best wishes
Gordon


> Or am I wrong here?
>
> Best Regards
> Adriaan
>
>
> 2014-02-02 Gordon K Smyth <smyth at wehi.edu.au>:
>
>> 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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