I was trying to do a Significance Analysis of Microarray data for some data (~20,000 genes x 8 total samples). My samples (n=4) belong to either of two groups (A and B). I have two replicates for each sample. So, my samples are:
I want to do a differential gene expression analysis. In the siggenes/SAM documentation, it doesn't mention replicates. How do I go about specifying the class labels?
Should I just use 1,2,1,2,1,2,1,2? Else, how should I specify the class label?