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Table 2 EzArray has built-in algorithms that help users select statistical testing methods based on the number of sample groups and replicates

From: EzArray: A web-based highly automated Affymetrix expression array data management and analysis system

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 statisticsUser 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
  1. While users can specify the statistical testing methods and parameters for the analysis, EzArray has built-in logics to select methods and parameters in the default modes. In general: 1) RMA is used to pre-process data; 2) If there is only one sample group, no analysis is performed; 3) If there are two groups and one or both of them has less than three replicates, then a fold change cut-off is applied, and the system returns the top genes (both up and down regulated, up to 100 in total) with 1.8 or higher fold change; 4) If there are three or more groups and one or more of them have less three replicates, then a Standard Deviation (SD) cut-off is applied, and the system returns the top genes (both up and down regulated, up to 100 in total) with SD within 90%; 5) If there are two groups and both of them have three or more replicates, then t test and Benjamini & Hochberg step-up FDR (BH) are applied, and the system returns the top 100 genes ordered by adjusted p-values, unadjusted p-values, and test statistics and with fold change >= 1.8; 6) If there are three or more groups and all groups have three or more replicates, then F-test and BH are applied, and the system returns the top 100 genes ordered by adjusted p-values, unadjusted p-values, and test statistics.