Hello, I have an experimental design comparing gene expression in 1) tissue that has been subjected to surgical treatment compared to 2) untreated tissue from the same mouse. Ordinarily I would think of doing a paired analysis for dCt(1) - dCt(2) to derive the ddCt and test whether it is significantly different from zero, and addressing the question whether there is a significant difference in expression between the two treatment conditions. However, this analysis will be done comparing 4 different genotypes, and I want to know whether there is a significant difference in the change in gene expression (tissue 1 vs tissue 2) depending on genotype. Can anyone please advise me on the best statistical model/test for these conditions? Thank you for your help.
