getOutliers: Get outliers for the different YAQCStatsObject slots

In yaqcaffy: Affymetrix expression data quality control and reproducibility analysis

Description

This function retrives the outliers fot the different quality control metrics stored in a YAQCStatsObject. Outliers are defined as being outside of the mean +/- 2 stdev range or mean/2, mean*1.5 for the scale factor.

Usage

  getOutliers(YAQCStatsObject,slot)

Arguments

YAQCStatsObject	an object of type "YAQCStats"
slot	an object of type string describing the slot for which the outliers should be retrieved (see details for possible slot strings)

Details

The slot strings that can be used are:

scale factor

"sfs"

average background

"avbg"

average noise

"avns"

percentage present

"pp"

β-actin 3'/5' ratio

"actin"

GAPDH 3'/5' ratio

"gapdh"

internal bioB control

"biob"

internal bioC control

"bioc"

internal bioD control

"biod"

Dap spike control

"dap"

Thr spike control

"thr"

Phe spike control

"phe"

Lys spike control

"lys"

Value

An object of type "numeric" giving the outliers names and values

Author(s)

Laurent Gatto

Examples

  ## load data
  library(MAQCsubsetAFX)
  data(refA)
  ## create the yaqc object
  qobj <- yaqc(refA[, 3:5])
  ## get outliers for the scale factor
  getOutliers(qobj, "sfs")

yaqcaffy documentation built on Nov. 8, 2020, 8:31 p.m.