**A.** Is the plotMDS function (from the limma package) based on PCA (Principal Component Analysis) or a PCoA (Principal Coordinate Analysis)?

**B.** What the values on the plot represent?
Is it **root-mean-square average** or

**root-mean-square deviation**(see below)?

In the limma paper published in Nucleic Acids Res at 2015 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4402510/) it is stated that: "Distances between samples on the plot represent ‘leading fold change’, which is defined as the

**root-mean-square average***of the log-fold-changes for the genes best distinguishing each pair of samples. "In the R manual it is stated that: "The distance between each pair of samples (columns) is the

**root-mean-square deviation**(Euclidean distance) for the top ‘top’ genes. Distances on the plot can be interpreted as _leading log2-fold-change_, meaning the typical (root-mean-square) log2-fold-change between the samples for the genes that distinguish those samples."

Thank you,

Arik

This video may be helpful for a basic understanding on this topic.

Sorry but the link does not work.

Should work now.