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Table 1 Results on simulated data for threshold setting based on desired FDR = 0.05.

From: Significance analysis of microarray transcript levels in time series experiments

 

Method 1

Method 2

Method 3

 

# selected genes

# FP/# sel.genes

# selected genes

# FP/# sel.genes

# selected genes

# FP/# sel.genes

M = 10

73

(17)

0.045

(0.027)

100

(8)

0.040

(0.014)

8

(10)

0.304

(0.334)

M = 30

91

(21)

0.078

(0.045)

120

(13)

0.059

(0.028)

83

(10)

0.098

(0.046)

M = 50

96

(16)

0.068

(0.024)

126

(12)

0.058

(0.021)

130

(12)

0.053

(0.027)

  1. All measurements were averaged across the 100 simulations; standard deviations are reported in parenthesis. Number of selected genes and number of false positives divided by the number of selected genes, obtained by applying the 3 methods on simulated data (setting α in correspondence to a desired FDR of 0.05).
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BMC Bioinformatics

ISSN: 1471-2105

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