Skip to main content

Table 1 False discovery rates for present and marginally present classifications

From: Correcting for sequence biases in present/absent calls

 

5%

10%

17%

 

P value

FP

TP

P value

FP

TP

P value

FP

TP

Raw PM and MM

0.008

1,098

19,398

0.025

2,291

20,182

0.060

4,300

20,687

GC-RMA PM and MM

0.024

1,127

20,013

0.111

2,372

20,607

0.216

4,136

20,944

GC-RMA MM threshold

0.037

1,107

19,969

0.111

2,392

20,621

0.235

4,202

21,003

  1. The number of false positives (FPs) and true positives (TPs) is for a given percentage of false positives out of the total number of positives (5%, 10% and 17% but percentages for each method are not exact due to P value granularity) and the corresponding P value cutoff for the MAS 5.0 present/absent calls. The calculations are based on a total of 60,624 true negatives (10,104 empty probesets in 6 replicates) and 23,436 true positives (3,906 probesets that can be aligned to transcripts in six replicates). The default P value cutoff is 0.060 for separating marginally present from absent transcripts.