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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 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
  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.