Hi All,

I am new to limma and R programming.

I have the CEL.files uploaded, normalised as an expression set, and have put together the target.txt file containing the following layout:
Name    FileName             Target   Date
5              0207_DaB7_H_ea_Blast1.CEL     blastocyst            13/02/2007
6              0207_DaB8_H_ea_Blast2.CEL     blastocyst            13/02/2007
4              0207_DaB6_H_ea_4cell_r3.CEL  4cell       16/02/2007
16           0307_DaB1_H_ea_oocyte_r1.CEL             oocyte  23/03/2007
17           0307_DaB3_H_ea_oocyte_r3.CEL             oocyte  23/03/2007
18           0307_DaB5_H_ea_4cell_r2.CEL  4cell       23/03/2007
21           1007_DaB4_H_ea_4cell_r1.CEL  4cell       24/10/2007
22           1007_DaB9_H_ea_Blast3.CEL     blastocyst            24/10/2007
23           1007_DaB21_H_ea_oocyte9856.CEL        oocyte  24/10/2007
24           1007_DaB22_H_ea_oocyte9858.CEL        oocyte  24/10/2007
1              0108_DaB18_H_ea_4cell_0.9_r4.CEL       4cell       10/01/2008
2              0108_DaB20_H_ea_4cell_0.9_r6.CEL       4cell       10/01/2008
3              0108_DaB23_H_ea_Blast_2.5_r4.CEL      blastocyst            10/01/2008
10           0213_SueK(2)4_H_ea_005_B4.CEL           blastomere         01/03/2013
14           0213_SueK(2)8_H_ea_005_B8.CEL           blastomere         01/03/2013
15           0213_SueK(2)10_H_ea_002_8CE.CEL      8cell       01/03/2013
7              0213_SueK(2)1_H_ea_005_B1.CEL           blastomere         06/03/2013
8              0213_SueK(2)2_H_ea_005_B2.CEL           blastomere         06/03/2013
9              0213_SueK(2)3_H_ea_005_B3.CEL           blastomere         06/03/2013
11           0213_SueK(2)5_H_ea_005_B5.CEL           blastomere         06/03/2013
12           0213_SueK(2)6_H_ea_005_B6.CEL           blastomere         06/03/2013
13           0213_SueK(2)7_H_ea_005_B7.CEL           blastomere         06/03/2013
19           0713_Suek(3)2_Ep_H_8C_006_11.CEL    8cell       02/07/2013
20           0713_Suek(3)3_Ep_H_8C_004_11.CEL    8cell       02/07/2013


But am struggling with setting up the design matrix and contrasts. My limited programming ability is probably playing the largest role, and I feel like smashing the computer against the wall (probably a sign of slight frustration )

The batch dates are included in the Target file, as I would like to add them as a factor when computing the T-test. But this isn’t a contrast I would like to make on its own (does that make sense?)

I would like to make all possible combinations of contrasts, listed as targets.

Any help would be fantastic!!!!!
Thank you in advance,
Helen




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