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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