Hi

I am new to Bioconductor R/Limma. I've worked through some examples,  
and familiarized myself with some basic commands. However, I am not  
sure how to create a model matrix for my experiment. We looked at  
three age groups of rats (YA, MA and OA) to look at gene expression  
changes following LTP (LTP is a memory model). LTP was stimulated on  
one side of the brain, while the opposite side served as control. So  
RNA from Control side was coupled to Cy3, while RNA from LTP side was  
coupled to Cy5. A single microarray was used for each animal, with n=5  
for YA, 3 for MA and 5 for OA. My Targets file looks as follows:

SlideNumber	Name	FileName	Cy3	Cy5
1	young	YA19_with norm_15Sept06.gpr	Ct	LTP
2	young	YA23_with genepix norm.gpr	Ct	LTP
3	young	YA 24_with norm.gpr	Ct	LTP
4	young	YA27_with norm_15Sept06.gpr	Ct	LTP
5	young	YA28_with norm_15Sept06.gpr	Ct	LTP
6	middleaged	MA3_with norm_15Sept06.gpr	Ct	LTP
7	middleaged	MA12_with norm_15Sept06.gpr	Ct	LTP
8	middleaged	MA15_with norm_15Sept06.gpr	Ct	LTP
9	aged	OA14_with norm.gpr	Ct	LTP
10	aged	OA 19_with norm.gpr	Ct	LTP
11	aged	OA 32_with genepix norm.gpr	Ct	LTP
12	aged	OA37_with norm_150906.gpr	Ct	LTP
13	aged	OA38_bal_15Sept06.gpr	Ct	LTP

How can I differentiate the groups in a model matrix? I would like to  
compare the gene expression changes between the three groups. I would  
have liked to look at the gene expression changes as a result of LTP  
in the individual groups too, but I have been warned recently that  
this might bring up more false positives since I do not have dye swaps  
within each group.

Thanks in advance.

Carthika
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