how to quantify outliers on multi-dimensional scaling plot?

Previous Topic Next Topic
 
classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

how to quantify outliers on multi-dimensional scaling plot?

anikaM
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

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.