[BioC] how to add contrast for lmFit in limma?

[Jianping Jin]

Dear list:

I am confused in how to add contrasts in the design table. I added "batch", 
RNA amplification batches, as a factor to see and or to try avoid batch 
effect on the results. The three factors are normal/disease, 
smoke/non-smoke, and batch 1/batch 2. I am interested to know if these 3 
variables have any effect on gene expression.

It appears to me that there is no way to use factor effects model (with 
intercept), which could make design easier. For the cell means model design 
as shown below there are so many combinations that needs to build contrasts 
and I am not sure of an efficient way.

I will greatly appreciate it if anyone could help me out!

The design is shown with the column notations as the following:
n: normal
p: patient
N: non-smoke
Y: smoke
1 and 2: batch

> design
   nN1 nN2 nY1 nY2 pN1 pN2 pY1 PY2
1    1   0   0   0   0   0   0   0
2    0   0   1   0   0   0   0   0
3    0   0   1   0   0   0   0   0
4    1   0   0   0   0   0   0   0
5    0   1   0   0   0   0   0   0
6    0   1   0   0   0   0   0   0
7    0   0   0   1   0   0   0   0
8    0   0   0   1   0   0   0   0
9    0   0   0   0   0   0   1   0
10   0   0   0   0   0   0   1   0
11   0   0   0   0   1   0   0   0
12   0   0   0   0   0   0   0   1
13   0   0   0   0   0   1   0   0
14   0   0   0   0   0   0   1   0
15   0   0   0   0   0   1   0   0
16   0   0   0   0   0   1   0   0
17   0   0   0   0   1   0   0   0
18   0   0   0   0   0   0   0   1
attr(,"assign")
[1] 1 1 1 1 1 1 1 1
attr(,"contrasts")
attr(,"contrasts")$treatment
[1] "contr.treatment"

For your convenience I listed the target below as well:

>> target
>          Sample Expt Smoke Batch
> 3  LCM_06CR.CEL    n     N     1
> 5   LCM_11A.CEL    n     Y     1
> 7   LCM_14A.CEL    n     Y     1
> 8  LCM_15BR.CEL    n     N     1
> 14  LCM_30A.CEL    n     N     2
> 15  LCM_32A.CEL    n     N     2
> 16  LCM_33B.CEL    n     Y     2
> 17  LCM_34A.CEL    n     Y     2
> 1   LCM_04A.CEL    p     Y     1
> 2   LCM_05A.CEL    p     Y     1
> 4  LCM_08BR.CEL    p     N     1
> 6   LCM_13B.CEL    p     Y     2
> 9  LCM_16B1.CEL    p     N     2
> 10  LCM_19A.CEL    p     Y     1
> 11  LCM_22B.CEL    p     N     2
> 12  LCM_24B.CEL    p     N     2
> 13  LCM_27A.CEL    p     N     1
> 18  LCM_37B.CEL    p     Y     2

Jianping

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x Jianping Jin Ph.D.            x
x Bioinformatics scientist      x
x Center for bioinformatics     x
x 3133 Bioinformatics Building  x
x CB# 7104                      x
x University of North Carolina  x
x Chapel Hill, NC 27599         x
x Tel: (919)843-6105            x
x Fax: (919)843-3103            x
x E-mail: jjin at email.unc.edu    x
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