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

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