Hi - I have two gene expression experiments that I performed on microarrays at different times:
expt 1: 3x untreated controls 3x treatment A
expt 2: 3x untreated controls 3x treatment B
note: the untreated controls are from the same RNA in both experiments.
Whilst I can easily determine treatment A and B effects separately, I would also like to find out what is statistically different between A and B. I can do a Venn diagram to see what is unique and common to both lists, but I was wondering whether there was a more statistical method.
I thought that perhaps I could normalise the treatment signals to the relative average control signal in each case, and then compare these ratios (A/CTRL vs B/CTRL) to each other in a t-test or similar.
Or make a joint experiment with all 12 samples and somehow construct a linear model to take into account the control groups measured twice.
Thanks for any help