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.