I have 2 files. first column will be the genes name and the other columns will be the cases with expression value for each gene in each case. in other word, the rows will be the expression values for the genes and the columns will be the case which represent the replicates. I am trying to find the differentially expression value for each gene between the two files. first file contains 300 replicates and the second file contains more than 400 replicates. I read the user guide SAGE profiles of normal and tumor tissue section and edgeR tutorial but they said I have to have only 2 columns. I would like to ask if there is any way to work with the whole files instead of divide then into 2 columns.