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Table 2 List of alternative parameters

From: Gene set analysis methods: a systematic comparison

Method Alternative Parameters
GSEA Calculating the FDR q-values based on the reported p-values as opposed to the q-values reported, which are based on the median.
SAFE Method: Bootstrap (‘Bootstrap.q’)
Global Statistic: aveDiff, FET, Pearson
Num. of Permutations (Pi.Mat): 10,000
sigPathway Not applicable
CAMERA Not applicable