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Table 1 Probe sets remaining 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

22,283

14,035

11,906

10,678

9,545

8,050

Average Signal

22,283

14,030

11,888

10,657

9,546

8,057

Overlap (MAS5)b

 

89%

89%

88%

87%

85%

Average RMA value

22,283

14,118

11,909

10,687

9,526

8,076

Overlap (RMA)c

 

77%

77%

77%

77%

77%

 

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

8799

4611

3981

3627

3237

2896

Average Signal

8799

4536

3988

3625

3231

2904

Overlap (MAS5)b

 

84%

84%

84%

83%

93%

Average RMA value

8799

4639

3984

3635

3229

2890

Overlap (RMA)c

 

73%

72%

72%

72%

71%

  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. bThe percent of probe sets in common retained by both fraction Present and average MAS5 signal filter. cThe percent of probe sets in common retained by both fraction Present and average RMA value filter.