Hi, there

I am sorry for for the sounded simple question, but how do I set up my control group when processing my data to be used for analysis?

Say I have 3 groups in triplicates (all extracted from Genome Studio), being:

**control** (C1, C2, C3); **Treatment A** (A1, A2 ,A3); and **Treatment B** (B1, B2, B3).

Now, I am able to load the files to R (using Beadarray package), together with the control (probes) table - it generates a **EListRaw** object. I am also able to run the **normalization (neqc)**, **fit linear model (lmFit)**, and **empirical Bayes analysis (eBayes)** with **no problems**. And as expected, you have 3 possible contrast analysis in there: C vs A, C vs B and A vs B.

However, here is my question, how do I compare A vs B where both are already normalized to the control, or put it more simple, **how do I compare log2(A/C) vs log2(B/C)**? Is there any function in R where I can do this?

Please, any help will be much appreciated.

Douglas