I have three gene expression matrices, one from blood one from tumor and one from normal adjacent tissue. I would like to correlate the expression of all rows (genes) in blood and tumor. The matrices are ordered so that they contain the same samples (colnames) and same genes (rownames). What is the best way to do this in R?
My aim is to to check of some of the genes that are highly expressed in blood are also up-regulated in the tumor samples. Since I only have one data set from blood I cannot make a differentially expression analysis on blood alone.