This is the aim of the analysis in Figure 8A and Figure 8—figure supplement 1D/E. The main claim is that the expression variation induced by these haplotypes in the transgenics is correlated with the expression variation of accessions carrying the same haplotypes. This conclusion only holds when one of the 9 haplotypes is excluded. The explanation given for excluding this haplotype is that the correlation goes up after removing this. I did a quick simulation study and found that using this algorithm you'd expect that the best correlation found by dropping each of the 9 pairs would be greater than 46% about 21% of the time even if there were actually no correlation at all. So, this is really not very strong evidence that the haplotype effects are similar. Certainly, the statement "We found that the PRO2+/INT6+ effects, as detected in transgenic experiments (R2 = 0.94), partially explain the FLM-ß expression variation in natural Arabidopsis accessions (R2 = 0.46)" is not supported, because this 46% number is only true when you exclude those accessions that don't fit.