hi, i am doing analysis for 10 breast cancer arrays (two color Agilent4x44 arrays) with limma,where Cy3 is normal and Cy5 is tumor.And all are biological replicates ,means all 10 arrays have been prepared from 10 different patients. there are two categories as nod negative and nod positive.Five arrays from nod negative(5 patients) and five are from nod positive(another 5 patients).I want to see the differentially regulated genes between two categories(NOD NEGATIVE vs NOD POSITIVE). i designed the target file as given below..I want to make it sure whether it is correct or not. SampleNumber FileName Cy3 Cy5 1 1135_NN.txt wt1 mu1 2 2157_NN.txt wt1 mu1 3 3159_NN.txt wt1 mu1 4 4171_NN.txt wt1 mu1 5 5179_NN.txt wt1 mu1 6 628_NP.txt wt2 mu2 7 758_NP.txt wt2 mu2 8 880_NP.txt wt2 mu2 9 993_NP.txt wt2 mu2 10 1096_NP.txt wt2 mu2 1 to 5 are nod negative and ,6 to 10 are nod positive. thanx. NEERAJ RANA JRF IISC BANGLORE(INDIA) [[alternative HTML version deleted]]