Effect of Cq1 setting on the point estimates and credible intervals of the fixed effects of stress in the coral dataset, according to the naive model.

The points are posterior means, the 95% credible intervals are denoted as dashed lines connecting upper and lower interval limits across genes, to better visualize changes in their width. (a) Comparison of the results based on formula-approximated Cq1 (“est.”) with analyses assuming the same inflated (40) or diminished (35) Cq1 for all genes. The three most affected genes are clect, chrom, g3pdh, and hsp16, which were so low-abundant in at least one of the experimental conditions such that many of their qPCR trials were empty. (b) Comparison between analyses with formula-based Cq1 (“est.”) and uniform Cq1 = 37 for all genes.