[BioC] EdgeR: artifacts on BCV plot

[Adriaan Sticker]

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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