flagSamplesCtrl: flagSamplesCtrl

In NanoStringQCPro: Quality metrics and data processing methods for NanoString mRNA gene expression data

Description

Flag samples based on the performance of their controls.

Usage

## S4 method for signature 'RccSet'
flagSamplesCtrl(rccSet, method = c("cutoffByMMAD",
  "cutoffByVar"), stringency = 4)

Arguments

rccSet	An RccSet object
method	Character string specifying the method for outlier detection: either "cutoffByMMAD" or "cutoffByVar".
stringency	Numeric value passed to the cutoff function specified by the method argument (see the 'd' argument of cutoffByMMAD and cutoffByVar).

Details

The method and stringency arguments determine a cutoff value used to flag outlier samples based on the interquartile range of negative and positive controls and in the slope of the linear fit of count versus input of positive controls. Outliers will also be flagged if their positive control scaling factor (see posCtrlNorm) is outside the NanoString recommended range (i.e. below 0.3 or greater than 3).

Value

A numeric vector giving the indices of samples with outlier values as described above.

Author(s)

Dorothee Nickles

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