[R] how to quantify outliers on multi-dimensional scaling plot?

[Ana Marija]

Hello,

I am in process of writing a grant where I am explaining my planned
methylation analysis using R software "minfi". In the text of the
grant I am mentioning looking for samples containing outliers in the
multi-dimensional scaling (MDS) plot
https://rdrr.io/bioc/minfi/man/mdsPlot.html . My question is: how to
more precisely define what is an outlier on a MDS plot? I know it is
not logFC like on volcano plot. Is there is a way to quantify distance
on MDA plot or it is just sufficient to say that samples that cluster
separately are outliers?

Here you can find a full workflow for minfi package including making MDS plots:
https://www.bioconductor.org/packages/release/workflows/vignettes/methylationArrayAnalysis/inst/doc/methylationArrayAnalysis.html

Thanks
Ana