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 ______________________________________________ R-help@r-project.org 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.
