Table 2.

Comparisons performed using Limma

Analyses	Comparison	Factors
Analysis 1	24 h - 1 h	treatment X genotype
	24 h - 6 h
	6 h - 1 h
Analysis 2	inoculated - control 24 h	pathogen X genotype
	inoculated - control 6 h
	inoculated - control 1 h
Analysis 3	(inoculated - control 24 h) - (inoculated - control 1 h)	pathogen X genotype
	(inoculated - control 24 h) - (inoculated - control 6 h)
	(inoculated - control 6 h) - (inoculated - control 1 h)

Summary of comparisons made in each of the three analyses; all analyses were performed separately for each combination of factors: genotype (SCS-BTA18-Q, SCS-BTA18-q) and treatment (E. coli, S. aureus and control treatment) in Analysis 1 or genotype (SCS-BTA18-Q, SCS-BTA18-q) and pathogen (E. coli, S. aureus) in Analysis 2 and Analysis 3.