qc.get.alpha1: Get or set the alpha values for the current QC environment

In simpleaffy: Very simple high level analysis of Affymetrix data

Description

Alpha1 and Alpha2 are used to define the P/M/A thresholds for detection calling algorithm see - detection.p.val. These are array dependent, these functions set or get their values. Tau is a constant parameter within the calculation and is not array specific.

Usage

 qc.get.alpha1()
 qc.set.alpha1(value)
 qc.get.alpha2()
 qc.set.alpha2(value)
 qc.get.tau()

Arguments

value

A double representing the alpha1 or alpha2 threshold for defining detection calls. See detection.p.val for more details.

Value

qc.set.alpha1 and qc.set.alpha2 return nothing. qc.get.alpha1 and qc.get.alpha2 return a double.

Author(s)

Crispin J Miller

References

http://bioinformatics.picr.man.ac.uk/

See Also

detection.p.val

Examples

  setQCEnvironment("hgu133plus2cdf")
  qc.get.alpha1()
  qc.get.alpha2()
  qc.set.alpha1(0.05)
  qc.get.alpha1()
  qc.set.alpha2(0.05)
  qc.get.alpha2()

simpleaffy documentation built on Nov. 8, 2020, 11:09 p.m.