. 2021 Feb 10;6(1):ysab008. doi: 10.1093/synbio/ysab008

Table 1.

Calculation of relative expression and comparison of calculation methods

Method	Relative expression			Prediction using model means (E^-ΔCt, C#_TetR/C#_16S)
	µ	LL ^a	UL ^a	KD	Control
log(E^ΔCt)^b	0.031	0.002	0.421	0.37	11.97
Outlier removed	(0.015)	(0.002)	(0.089)	(0.17)	(11.81)
log(C#_TetR/C#_16S)^b	0.028	0.002	0.409	0.56	19.69
Outlier removed	(0.013)	(0.002)	(0.082)	(0.26)	(19.39)
lm(log(C#_TetR/C#_16S))^c	0.028	0.003	0.249	0.56	19.68
Outlier removed	(0.013)	(0.003)	(0.052)	(0.25)	(19.68)
glm.nb(C#_TetR/C#_16S)^c	0.155	0.027	0.883	4.99	32.29
Outlier removed	(0.009)	(0.004)	(0.025)	(0.30)	(32.29)

^{^a}

Lower and upper limit of 95% confidence intervals.

^{^b}

Analysis performed with SigmaPlot 13.0 ANCOVA analysis, using the Holm–Sidak method.

^{^c}

Analysis performed in R using linear models (lm from package stats) (34) and generalized linear models, with negative binomial (glm.nb from package MASS) (35) models, where Confint from car package (36) found the CIs. Values in brackets are results when removing the potential outlier from model data set (KD biological replicate 1, day 5). For reference, arithmetic means of E^−ΔCt are 3.12 and 20.05 for KD and control samples, respectively; and of C#_TetR/C#_16S are 5.22 and 33.69 for KD and control samples, respectively. See Supplementary Text for full details of analyses.