Table 3.

Analysis of variance (ANOVA) with a blocking factor. Hypothetical data are used to demonstrate an ANOVA for four individuals serving as the replicates spread across two qPCR plates. The qPCR plates serve as a statistical blocking factor. * = expression ratio significantly different from 1

Biological replicate	Group A ${\mathrm{\Delta }C}_{q;r,A}^{\left(w\right)}$	Group B ${\mathrm{\Delta }C}_{q;r,B}^{\left(w\right)}$	Group C ${\mathrm{\Delta }C}_{q;r,C}^{\left(w\right)}$	qPCR plate	Bonferroni-adjusted P-value
r = 1	0.855	1.203	0.866	1
r = 2	0.711	1.056	0.799	1
r = 3	0.582	0.890	0.522	2
r = 4	0.699	0.775	0.669	2
Source	Df	MS	F	P
Group	2	0.096	12.864	0.003
Plate Blocking	1	0.153	20.487	0.002
Error	8	0.007
Post-hoc testing	Mean Difference ${\mathrm{\Delta \Delta }C}_q^{\left(w\right)}$	95% C.I. for ${\mathrm{\Delta \Delta }C}_q^{\left(w\right)}$	Expression Ratio ${10}^{-\mathrm{∆∆}{C}_q^{\left(w\right)}}$	95% C.I. for ${10}^{-\mathrm{∆∆}{C}_q^{\left(w\right)}}$
Group A vs. B	−0.269	(−0.128, −0.410)	1.86	(1.34, 2.57)	0.007*
Group A vs. C	−0.002	(0.139, −0.143)	1.00	(0.726, 1.39)	1.000
Group B vs. C	0.267	(0.408, 0.126)	0.54	(0.391, 0.748)	0.007*