I've about 60 samples divided in two predefined groups (group A, group B). We perform gene expression analysis on these samples and wanted to know if the predefined groups reflects well (or not) the current expression profiles (we perform some clustering on it). In other terms the 60 samples will be grouped using the predefined groups (A or B - based on multiple clinical factors independent of expression profile) and also using the expression data (a clustering based on a big 60x20000 expression matrix). How can I assess that the clustering using the expression profiles are in concordance with the predefined groups.
I thought at a permutation approach were I permute at each iteration the sample groups assignment but I'm not sure if it's the right direction to choose.. Any ideas ?