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Table 2 Detection rates for the six gene set analysis methods on simple simulated data.

From: Microarray-based gene set analysis: a comparison of current methods

 

PCOT2

SAFE

GSEA-Category

GSEA-limma

Globaltest

sigPathway

On-Off (D)

0.902

0.236

0.912

0.24

0.93

0.002

 

(0.013)

(0.021)

(0.012)

(0.019)

(0.011)

(0.002)

On-On (D)

0.858

0.22

0.85

0.268

0.886

0

 

(0.016)

(0.019)

(0.014)

(0.019)

(0.014)

(0)

Off-Off (ND)

0.994

1

0.996

1

0.992

0.998

 

(0.003)

(0)

(0.003)

(0)

(0.005)

(0.002)

On-On (ND)

0.99

1

0.994

1

0.992

1

 

(0.004)

(0)

(0.003)

(0)

(0.004)

(0)

  1. 100 data sets (each containing 20 genes in 20 sets) were analyzed by each method, with 10,000 permutations used to generate p-values to which FDR controlling adjustments [21] were made. An adjusted p-value of 0.05 was required for significance. The value in each cell relates to the proportion of each type of gene set activity correctly identified by each method. Standard errors are shown in parentheses.