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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.
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