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Table 2 Highly significant (p ≤ 0.001) probe sets lost at different filtering thresholdsa.

From: Effects of filtering by Present call on analysis of microarray experiments

 

Unfiltered (total)

FP>0

sig254

RMA4.25

FP25

sig375

RMA4.75

FP50

sig475

RMA5.03

FP75

sig593

RMA5.30

FP100

sig795

RMA5.65

IFN Data

      

Fraction Present (MAS5)

1230

20

30

49

84

165

Average Signal (MAS5)

1230

8

26

43

57

112

Fraction Present (RMA)

1641

53

92

143

218

334

Average RMA (RMA)

1641

92

161

205

252

346

 

Unfiltered (total)

FP>0

sig200

RMA5.05

FP25

sig265

RMA5.47

FP50

sig323

RMA5.70

FP75

sig400

RMA5.95

FP100

sig475

RMA6.17

Vitamin A Data

      

Fraction Present (MAS5)

168

8

10

10

14

17

Average Signal (MAS5)

168

5

9

13

19

24

Fraction Present (RMA)

177

5

7

10

14

18

Average Signal (RMA)

177

13

17

22

28

31

  1. aFor comparison of different filters, thresholds were selected for each filter that removed similar number of probe sets. Types of filter: Fraction Present, 'FP' followed by threshold value; Average MAS5 signal, 'sig' followed by signal threshold; average RMA value, 'RMA' followed by threshold value. Total number of probe sets with p ≤ 0.001, followed by the number removed at each threshold (cumulative).