Sample Groups | Sample Replicates | Basic Statistical Method | Multiple Testing Procedure | Gene (feature) Limit Options | Main result files |
---|---|---|---|---|---|
1 | Any | None | None | None | None |
2 | < 3 in either group |
• Average values of each gene (feature) within group • Calculate fold change of each gene between groups | None |
1. Fold Change 2. Total number of genes 3. User gene list |
• Gene list • Fold changes • Expression values • Heatmap of top genes |
≥3 in both groups |
• two-sample Welch t-test (unequal variances) • two-sample t-test (equal variances) • standardized rank sum Wilcoxon test • paired t-test • Options for Raw/Nominal p-value calculation: - Parametric - Permutation - Options for Side/Rejection Region: abs, upper, lower |
• Bonferroni single-step FWER • Holm step-down FWER • Hochberg step-up FWER • Sidak single-step FWER • Sidak step-down FWER • Benjamini & Yekutieli step-up FDR • Benjamini & Hochberg step-up FDR – selected • Storey q-value single-step pFDR • Westfall & Young maxT permutation FWER • Westfall & Young minP permutation FWER |
• Fold Change • Limit to - Total number of genes - adjusted p-values - raw p-values - test statistics • User gene list |
• Gene list • Fold changes • Statistic • Raw p-values • Adjusted p-values • Expression values | |
≥3 | ≤3 in any group |
• Calculate percentile of standard deviation (SD) of each gene cross all samples • Select genes by a SD percentile cutoff |
• Standard Deviation (SD) • Total number of genes • User gene list |
• Gene names • Standard Deviation • Expression values | |
≥3 in all groups |
• F-test • Block F-test • Options for Raw/Nominal p-value calculation: - Parametric - Permutation - Options for Side/Rejection Region: abs, upper, lower |
• Bonferroni single-step FWER • Holm step-down FWER • Hochberg step-up FWER • Sidak single-step FWER • Sidak step-down FWER • Benjamini & Yekutieli step-up FDR – selected • Benjamini & Hochberg step-up FDR • Storey q-value single-step pFDR • Westfall & Young maxT permutation FWER • Westfall & Young minP permutation FWER |
• Total number of genes • User gene list |
• Gene names • Statistic value • Expression values |