Table 3 The number, identity (Flybase gene number), log fold-change (logFC), adjusted p-value or FDR, of genes identified as differentially expressed (DE) between each treatment and the symbiont-free control, by each of the four methods utilized. Results are shown for analyses of both genes and exons. Only the Hyd1 treatment exhibited significant DE genes.

	Deseq 2						EdgeR						EdgeR		LimmaVoom
	by Gene			by Exon			glm (TMM) by gene			glm (TMM) by exon			qlglm (TMM) by gene	qlglm (TMM) by exon	TMM + voom by gene	TMM + voom by exon
Treatment (number of replicates)
MSRO (4)	None			None			None			None			None	None	None	None
wMel (3)	None			None			None			None			None	None	None	None
Hyd1 (3)	7			12			5			5			None	None	None	None
	FlyBaseGeneNo.	Log FC	adjusted p	FlyBaseGeneNo.	Log FC	adjusted p	FlyBaseGeneNo.	Log FC	FDR	FlyBaseGeneNo.	logFC	FDR
	FBgn0038339	−4.97	0.000087	FBgn0038339	−4.96	0.000086	FBgn0038339	−4.90	0.002497	FBgn0038339	−4.89	0.002948
	FBgn0000451	−4.57	0.000151	FBgn0000451	−4.53	0.000253	FBgn0000451	−4.54	0.030333	FBgn0000451	−4.50	0.030877
	FBgn0027527	−4.81	0.006198	FBgn0027527	−4.81	0.005639	FBgn0027527	−4.77	0.030344	FBgn0027527	−4.78	0.030877
	FBgn0037099	−6.66	0.027599	FBgn0037099	−6.66	0.021794	FBgn0037099	−6.29	0.030344	FBgn0037099	−6.30	0.030877
	FBgn0037414	−4.56	0.008411	FBgn0037414	−4.55	0.006991	FBgn0037414	−4.53	0.035559	FBgn0037414	−4.52	0.041176
	FBgn0001254	−3.51	0.006703	FBgn0001254	−3.51	0.005761	FBgn0001254*	−3.50	0.076620
	FBgn0001256	−3.98	0.009660	FBgn0001256	−3.98	0.007762	FBgn0001256*	−3.96	0.084605
				FBgn0029807	−4.23	0.026208
				FBgn0000568	−0.99	0.049803
				FBgn0262366	2.90	0.049803
				FBgn0035430	−3.80	0.049803
				FBgn0033275	−3.77	0.005761

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