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

[Sean Davis]

On Saturday 04 November 2006 13:20, Kimpel, Mark William wrote:
> 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?

This can't be handled with a linear model?

Sean