Better late than never:

If you have processed your data by the Robust MultiArray Average (RMA) method and your array is single-colour, then your data is already log [base 2] (log2) transformed. Proceed with analyses via Limma, which will derive log2 ratios for you, coupled with p-values.

If your array is 2-colour, then your data is already representative of log2 ratios between colour 1 vs. colour 2. The analysis approach in this case may differ; however, it's more than likely that you have a single colour array.

Note that the calculation is this:

a=c(1,2,3,4,5)
b=c(4,5,6,7,8)

log2(mean(b) / mean(a))
[1] 1

...or this:

log2(mean(b)) - log2(mean(a))
[1] 1

Kevin