Effect of <i>Cq</i>1 setting on the point estimates and credible intervals of the fixed effects of stress in the coral dataset, according to the naive model.

<p>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 <i>Cq</i>1 (“est.”) with analyses assuming the same inflated (40) or diminished (35) <i>Cq</i>1 for all genes. The three most affected genes are <i>clect</i>, <i>chrom</i>, <i>g3pdh</i>, and <i>hsp16</i>, 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 <i>Cq</i>1 (“est.”) and uniform <i>Cq</i>1 = 37 for all genes.</p>