Dear all, I have a problem in understanding the contrast matrix in analyzing the microarray data. When slecting the differentially expressed gene in one case, I am using the following contrast matrix S48-C48 S27-C27 bss-bsc bts-btc C48 0 0 0 0 S48 0 0 0 0 C27 0 0 0 0 S27 0 0 0 0 bsc 0 0 -1 0 bss 0 0 1 0 btc 0 0 0 -1 bts 0 0 0 1 when counted for coeff 3 and coeff 4, I am getting a set of gene as 60 for coeff 3 and 58 for coeff 4 While using same data with the following contrast matrix bss-bsc bts-btc bsc -1 0 bss 1 0 btc 0 -1 bts 0 1 I am getting 580 for coeff 1 and 550 for coeff 2. I am not able to understand what is the problem here as both the coeff i am asking is same but still i get different results for two contrast matrix Is something i am missing in understanding the principle of making the contrast. Somebody please help in understanding the problem here, I shall be very thankful for your kind help. Best Wishes -- Hemant Ritturaj Kushwaha [[alternative HTML version deleted]]