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Sets

MSPC classifies peaks under Background, Weak, Stringent, Confirmed, Discarded, True-Positive, and False-Positive categories. (Refer to method description for details.) The following figure is a schematic view of these categories and their relation.

SetsSets

(The number of ERs in different sets reported in this figure, are the result of wgEncodeSydhTfbsK562CmycStdAlnRep1 and wgEncodeSydhTfbsK562CmycStdAlnRep2 (available for download from Sample Data page) comparative analysis using -r bio -w 1e-4 -s 1e-8 parameters.)

Background​

Peaks with p-value >= weak threshold.

Weak​

Peaks with stringency threshold<= p-value <weak threshold.

Stringent​

Peaks with p-value < stringency threshold.

Confirmed​

Peaks that:

  1. are supported by at least c peaks from replicates, and
  2. their combined stringency (xSquared) satisfies the given threshold: xSquared >= the inverse of the right-tailed probability of Gamma and
  3. if technical replicate, passed all the tests, and if biological replicate, passed at least one test.

(see method description)

Discarded​

Peaks that:

  1. does not have minimum required (i.e., c) supporting evidence, or
  2. their combined stringency (xSquared) does not satisfy the given threshold, or
  3. if technical replicate, failed a test.

TruePositive​

The confirmed peaks that pass the Benjamini-Hochberg multiple testing correction at level alpha.

FalsePositive​

The confirmed peaks that fail Benjamini-Hochberg multiple testing correction at level alpha.

See Also​