[BioC] Regression analysis using expression microarray to determine phenotypic correlation

[Ruppert Valentino]

Hello,
 
I have a question regarding regression analysis using gene expression microarrays. I have microarray data of 16 arrays. Each 4 arrays can be grouped by a mutation in a gene so we will have something like this:
 
Patient 1-4     Mutation in Gene A
Patient 5-8     Mutation in Gene B
Patient 9-12    Mutation in Gene C
Patient 13-16   Mutation in Gene D
 
 
 
My question is can use regression analysis to determine whether the groups with phenotype MutA correlates with say MutC? or whether MutA and MutB correlates with MutC? ..etc.
 
If its possible to do this what the best bioconductor package to use? and would it give a p value to test the correlation between the various phenotypes?
 
 
Many thanks
 
 
Ruppert