10.1371/journal.pone.0071448.g002 Mikhail V. Matz Mikhail V. Matz Rachel M. Wright Rachel M. Wright James G. Scott James G. Scott 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. Public Library of Science 2013 Biochemistry Nucleic acids dna DNA amplification Computational biology Molecular genetics gene expression genetics genomics Functional genomics Marine biology corals Molecular cell biology estimates credible intervals coral naive 2013-08-19 02:36:51 Figure https://plos.figshare.com/articles/figure/_Effect_of_Cq_1_setting_on_the_point_estimates_and_credible_intervals_of_the_fixed_effects_of_stress_in_the_coral_dataset_according_to_the_naive_model_/775814 <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>