[BioC] edgeR: plotBCV, gof() and plotMDS, for outlier detection

Ryan rct at thompsonclan.org
Mon Mar 3 09:01:34 CET 2014

That BCV plot looks bizarre, with the two bands. What does the BCV plot 
look like if you exclude the outlier sample? Does the double-banding go 
away? Does the prior.df change?

Regardless, I think it's pretty clear from the MDS that this sample is 
an outlier and should probably be excluded from your analysis.

On Sun Mar  2 12:00:50 2014, Sindre Lee wrote:
> Hello!
> I have been struggling with one of the skeletal muscle biopsies in my
> study. The RNA quality is very good and looking at tissue specific
> gene expression they are all there, although some with very different
> values for some genes compared the other biopsies.
> Please see the attached plots using edgeR. The gof() calculation gave
> 0 "TRUE" in the $outlier table.
> Can anyone shed some light on this? Thank you very much.
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