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 |