Could you give me a hint how to make 2d or better 3d plots where two or more separated groups of conditions can be shown? My data set looks like this:
Gene CON1 CON2 CON3 condiditons 17 in totoal -->
genes 116 rows in total
Table id filled with expression intensities. How should I calculate distances between conditions based on expresion intensites? At this moment I made plots with two groups when every point was a gene(116 points) but I'd like to do this for conditions.
Some hints : MDS plots with R
Limma has a function plotMDS as well as CummeRbund, I have used the one from CummeRbund works well.
I have a write-up for PCA and MDS here https://rpubs.com/crazyhottommy/PCA_MDS
Great tutorial, thanks for help, I get what I need ;)