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Helen Smith
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100
@helen-smith-6087
Last seen 10.2 years ago
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 ï)
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 isnât 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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