Table 1:

Statistics

FigureData structureType of testType I error controlNotes
1BGene counts for differential expression analysisModerated t tests with linear regression (empirical Bayes)FDR < 0.1limma Bioconductor package: voom approach
1CGene set enrichment analysisHypergeometric testFDR < 0.05clusterProfiler Bioconductor package: compareClusters approach
1DNormalized qPCR dataStudent's t testp < 0.05 
2BNormalized qPCR dataStudent's t testp < 0.05 
2CGene counts for differential expression analysisModerated t tests with linear mixed effects modeling (empirical Bayes)Bonferroni < 0.05limma Bioconductor package: voom approach
2DGene set enrichment analysisHypergeometric testFDR < 0.05clusterProfiler Bioconductor package: compareClusters approach
2ENormalized qPCR dataStudent's t testp < 0.05 
3BNormalized qPCR dataStudent's t testp < 0.05 
3CDifferential expression analysisModerated t tests with linear regression (empirical Bayes)FDR < 0.05limma Bioconductor package: voom approach
3DGO enrichment analysisHypergeometric testFDR < 0.05clusterProfiler Bioconductor package: compareClusters approach
4ANormalized qPCR dataStudent's t testp < 0.05 
4BNormally distributedStudent's t testp < 0.05