[BioC] EdgeR: artifacts on BCV plot

[Gordon K Smyth]

Dear Adriann,

It isn't an artifact.  You are simply seeing a few genes for which the 
dispersion is estimated to be zero.  EdgeR puts these dispersions to a 
small positive value.  They are not harmful.

You could also try

   estimateDisp()

which will automatically estimate the prior df for you.  This function 
also has a robust option.  If you turn it on, then it will ensure that 
large or small tail dispersions don't affect the other dispersions. 
However I doubt this is serious problem for you.

Best wishes
Gordon

> Date: Thu, 30 Jan 2014 18:23:23 +0000
> From: Adriaan Sticker <adriaan.sticker at gmail.com>
> To: bioconductor at r-project.org
> Subject: [BioC] EdgeR: artifacts on BCV plot
>
> Hi all,
>
> I made some BCV plots of my data after the tagewise estimation step. I
> notice sometimes that I gave genes with identical very low BCV values .It
> appears as a horizontal line below the rest of my data but it is always
> above zero. I put an example in attachement. They disapear when I higher
> the cutoff of my filter (cpm(counts)>1 to  cpm(counts)>2) but then I also
> lose a fraction of my genes.
>
> I wonder how I should interpret these values? What are they exactly. My
> guess would be that they are very low counts and due the discretness of
> count data, their bcv is zero?
> If I dont up my filter cutoff and thus leave them in the data, how harmfull
> are they? Can they influence much the estimation of BCV of the other data?
> (I use prior.df = 20) I can see the trended dispersion line moving a bit
> when I up my filter for the lower counts.
>
> In attachement the BCV plot with the artifacts (cpm(counts)>1) and a BCV
> plot without them (cpm(counts)>2)
>
> Best regards
> Adriaan Sticker
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