I have count data from a RNAseq experiment (2 samples are from normal cells and 3 samples are cells with a disease), and the data is already standardized by trimmed mean of M values (TMM). I want to do some plots: biplot of Principal Component Analysis (PCA) and a cluster dendrogram to see if the samples normal/disease are well separated (there is a clear difference between them). Since the data is already standardized (TMM) should I scale and center the data prior to perform PCA and cluster dendrogram??
thank you!