[BioC] Differential Gene Expression using limma

[Sonia SHAH]

Hi,

It would be greatly appreciated if I could get some advice on how to go
about looking at differential expression on my data.

I have Affy data from 3 different cell types: type1, type2, type3
and 3 biological reps for each type


I want to get 2 gene lists using limma:
1. genes that are expressed in type1 and type3 but not in type2
2. genes that are expressed in type2 and type3 but not in type1

There seem to be lost of different ways of doing this. I tried 2 design
matrices:

DESIGN1
		type1	type2	type3
type1rep1	1	0	0	
type1rep2	1	0	0
type1rep3	1	0	0
type2rep1	0	1	0
type2rep2	0	1	0
type2rep3	0	1	0
type3rep1	0	0	1
type3rep2	0	0	1
type3rep3	0	0	1

contrasts: (type1+type3)-type2
	    (type2+type3)-type1



DESIGN2
I would use 2 design matrices to get each gene list

The first matrix below will give genes that are in type1+3 but not in
type2:

		A	B
type1rep1	1	0		
type1rep2	1	0	
type1rep3	1	0	
type2rep1	0	1	
type2rep2	0	1	
type2rep3	0	1	
type3rep1	1	0	
type3rep2	1	0	
type3rep3	1	0	

contrast A-B


The second matrix below will give genes that are in type2+3 but not in
type1:

		A	B
type1rep1	0	1		
type1rep2	0	1	
type1rep3	0	1	
type2rep1	1	0	
type2rep2	1	0
type2rep3	1	0	
type3rep1	1	0	
type3rep2	1	0	
type3rep3	1	0	

contrast A-B


I would have thought that the two different approaches would give me the
same number of differentially expressed genes. But it doesn't. It gives
me very different numbers. 

Are the two approaches the same or am I doing something completely
wrong?




Thanks

Sonia