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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.