Hi folks, I am fairly new to limma. I hope that someone could help me out with a design metrix and contrast. Factors are: 1st - drug response (responder versus non-responder); 2nd - treatment time (each patient have two time points 0 week-sample collected before treatment versus 24 weeks- sample collected after treatment ). 3rd - batches. My questions: 1, I would like to find the drug responding genes. 2, should this be a two factor problem factors? how to handling paired samples? Thanks in advance, Steve This is my case, > targets filename responder time patients batch 1 PS_MN_B3_12 non 0 n1 B 2 PS_MN_B4_16 non 24 n1 B 3 PS_MN_D9_370 non 0 n11 D 4 PS_MN_D10_373 non 24 n11 D 5 PS_MN_D11_418 non 0 n12 D 6 PS_MN_D12_422 non 24 n12 D 7 PS_MN_E3_436 non 0 n13 E 8 PS_MN_E4_439 non 24 n13 E 9 PS_MN_E5_442 non 0 n14 E 10 PS_MN_E6_446 non 24 n14 E 11 PS_MN_E9_526 non 0 n17 E 12 PS_MN_E10_530 non 24 n17 E 13 PS_MN_E11_561 non 0 n18 E 14 PS_MN_E12_565 non 24 n18 E 15 PS_MN_B5_17 non 0 n2 B 16 PS_MN_B6_19 non 24 n2 B 17 PS_MN_B7_21 non 0 n3 B 18 PS_MN_B8_25 non 24 n3 B 19 PS_MN_B9_93 non 0 n4 B 20 PS_MN_B10_97 non 24 n4 B 21 PS_MN_B11_105 non 0 n5 B 22 PS_MN_B12_109 non 24 n5 B 23 PS_MN_C3_151 non 0 n6 C 24 PS_MN_C4_153 non 24 n6 C 25 PS_MN_C9_232 non 0 n7 C 26 PS_MN_C10_235 non 24 n7 C 27 PS_MN_C11_285 non 0 n8 C 28 PS_MN_C12_289 non 24 n8 C 29 PS_MN_D3_333 non 0 n9 D 30 PS_MN_D4_338 non 24 n9 D 31 PS_MN_B1_5 res 0 r1 B 32 PS_MN_B2_9 res 24 r1 B 33 PS_MN_F1_568 res 0 r10 F 34 PS_MN_F2_571 res 24 r10 F 35 PS_MN_F3_574 res 0 r11 F 36 PS_MN_F4_577 res 24 r11 F 37 PS_MN_C1_117 res 0 r2 C 38 PS_MN_C2_121 res 24 r2 C 39 PS_MN_C5_159 res 0 r3 C 40 PS_MN_C6_164 res 24 r3 C 41 PS_MN_C7_225 res 0 r4 C 42 PS_MN_C8_230 res 24 r4 C 43 PS_MN_D1_315 res 0 r5 D 44 PS_MN_D2_319 res 24 r5 D 45 PS_MN_D5_339 res 0 r6 D 46 PS_MN_D6_344 res 24 r6 D 47 PS_MN_D7_352 res 0 r7 D 48 PS_MN_D8_356 res 24 r7 D 49 PS_MN_E1_423 res 0 r8 E 50 PS_MN_E2_427 res 24 r8 E 51 PS_MN_E7_501 res 0 r9 E 52 PS_MN_E8_505 res 24 r9 E [[alternative HTML version deleted]]