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Table 1 Compared competitive gene set analysis methods

From: Robust multi-group gene set analysis with few replicates

Compared methods

Permutation type

Descriptions

 

mGSZm

sample

mGSZ from R package mGSZ updated with Perm4

 

mGSA

sample

Gene Set Z-score based gene set analysis method similar to GSA [17]

 

Allez

parametric

Allez from R package allez [14]

 

wKS

sample

wKS from R package mGSZ [16]

 

GAGE

parametric

Generally applicable gene set enrichment from R package gage [21]

 

CAMERA

parametric

Correlation adjusted mean rank gene set test from R package limma [13]

 

QuSAGE

parametric

Quantitative set analysis of gene expression from R package qusage [22]

 

romer

sample

Rotation testing using mean ranks from R package limma [24, 25]