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Table 1 List of default parameters

From: Gene set analysis methods: a systematic comparison

Method

Default Parameters

GSEA

Data File: Inputted txt file

Response File: Inputted txt file

Knowledge base: mSigDB gmx file

Num. Permutations: 1000

Permutation Type: Gene or Phenotype

Scoring Scheme: Weighted

Ranking Metric: Signal To Noise

SAFE

Data Matrix (X.mat): Inputted rda file

Response Vector (y.vec): Inputted rda file

Gene Category Assignments (C.mat): Created from gmt file

Method: Permutation

Min Category Size: 2

Max Category Size: Inf

by.gene: FALSE

Local Statistic: Student T-Test (“t.Student”)

Global Statistic: Wilcoxon Rank Sum (“Wilcoxon”)

Args.global: list(one.sided = F)

Num. of Permutations (‘Pi.mat’): 1000

Multiple Testing Correction (‘error’): FDR.BH

sigPathway

Data File: Inputted rda file

Knowledge base: mSigDB gmx file

Min gene set size: 1

Max gene set size: 10,000

allPathways: TRUE

Number of Pathways: length(mSigDB gmx file)

CAMERA

Data File: Inputted rda file

Response Inputted rda file

Knowledge base: mSigDB gmx file