[BioC] 2x2 factorial design in limma

[Kimpel, Mark W]

I am trying to use limma for the analysis of 2DGE proteomic data and am
having great difficulty constructing the design and contrast matrices
for a 2x2 factorial experiment. A small section of the data spreadsheet
is below. I have extracted all sorts of objects from this spreadsheet
including a matrix of only the data, a matrix of the factors, factor
names, etc. What I have not been able to do is figure out how to
translate those into the required design and contrast matrices. I am
interested in the main effects of the 2 factors as well as the
interaction between them.
 
Any help, including code samples, is greatly appreciated!
 
Thanks,
Mark W. Kimpel MD
Indiana U. School of Medicine,
Indianapolis, IN
 
 
Experiment
Keratinocytes: Nutrition, JP8 2x2 Design
 
 
 
 
Factor
Nutrition
High
High
Low
High
Low
High
High
Factor
JP8.vs.H2O
H2O
H2O
H2O
Jp8
Jp8
H2O
JP8
Sample.ID
may1501g-3390
may1501e-3391
may1501h-3392
may1501l- 3393v1
may1501n-3394
may1501q-3395
may1501b-3396
 
Spot.Number
 
 
 
 
 
 
Data.start
14
776.39
1136.96
847.86
1211.93
1366.17
1247.95
627.66
 
17
765.35
720.84
705.24
624.39
668.91
759.81
639.89
 
19
244.53
274.41
188.65
251.76
287.13
-1
168.21
 
21
140.24
214.14
116.44
181.11
264.72
166.28
175.97
 
22
647.23
802.11
256.37
630.47
1046.78
717.15
1196.63
 
27
274.84
389.64
459.78
701.53
722.04
720.45
191.88
 
103
493.72
412.51
400.92
295.2
432.94
390.06
450.54
 
105
271.05
189.73
413.47
266.26
-1
-1
-1
 
106
1451.17
1390.25
1215.72
1506.79
1427.72
1321.7
1876.38
 
107
-1
215.85
-1
113.77
-1
151.19
-1
 
108
145.56
304.96
244.99
621.74
525.55
663.87
225.03
 
109
6422.49
7251.3
6418.58
5977.25
6685.45
6098.35
6482.68
 
 
 
 
 

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