MDS plot: What is criteria to determine similarities and differences between the samples?

Question

[ygowtha]

Hello All

Can someone please explain on what basis the MDS plot is created in edgeR? I do understand that it helps to visualize the similarities and differences between the samples and replicates. But does it calculate the difference between these samples through the read profiles of genes?

Additionally, I would like to know what the dimensions of MDS plot refer to and an explicit way of knowing them in edgeR. Are they representative of the treatments used? I have not been able to get answers specific to my question. I apologize if my question is redundant, in which case, please direct me to the post/website that has the answer to my questions.

Thank you very much.

Answer 1

[Devon Ryan]

Please just read through the Wikipedia article on multidimensional scaling.

Edit: BTW, you might also read up on principal component analysis. The two are related ideas.

Answer 2

[dariober]

This video, A layman's introduction to principal component analysis, is very short & simple but useful to get the idea.