[BioC] microarray analysis of a dose response * strain experiment

[Kimpel, Mark William]

My group is writing a grant with a proposed dose response experiment on two different rat strains that I have been tasked to provide an analysis method for. Briefly, we have two rat strains that have different preferences for alcohol (one drinks, the other doesn't). We are going to give each line injections for alcohol to see if gene expression in the brain is differentially affected between the 3 strains. We don't, however, know which of several possible doses of alcohol will provide the greatest effect on each of the thousands of genes on our Affy chipset. So, we are proposing to give each line one of 4 doses (zero, 0.5, 1.0, and 2.0 mg/kg). For any gene, we have no way of knowing a priori what shape the dose response curve will take. We are, for screening purposes, not really interested in the shape of the curve, only that it is not a line with a slope of zero (i.e. no response). We are also, for screening purposed, only interested to know, for each gene, if the response of strain A is different from strain B. In other words, what we want to know is the interaction between strain and dose response.

I have searched the literature and the Bioconductor mailing list and cannot find a reference to an experiment of this sort. Can anyone provide some advice?

Thanks,

Mark

Mark W. Kimpel MD 

 
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