I cannot figure out the appropriate way to analyze the relative expression of genes in different brain regions with different behaviors. There are papers that have done these analyses, but they do not clearly state whether they used deltaCt's or deltadeltaCt's. Has anyone done these analyses before? I am particularly interested in individual differences in expression.
Sorry, I just looked at my question and realized I didn't include enough information. I used the ddCt values for all pairwise comparisons. What I meant is which value should be used when assessing the correlation between expression and a behavior e.g., is gene x correlated with locomotion using pearson's product moment correlation. I have found publications that use the dCt for this analyses and what I suspect is 2^-ddCt. Is one more correct than the other?
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