Hi, I'm trying to use limma to get a list of differentially expressed genes between subtypes (GCB and ABC) of B-cell lymphoma. I have a dataset from an Affymetrix array with gene expression reads for 271 samples. 71 of which were classified as ABC, 144 as GCB and 56 were unclassified.
I've managed to read my CEL files and perform normalisation on the gene expression data:
norm.batch = rma(batch) dat = exprs(norm.batch)
But I'm just not sure where to start with creating a design matrix for the limma analysis