negativeControl: Acessor functions for the 'negativeControl' slot in a...

In Shedimus/NanoStringDiff: Differential Expression Analysis of NanoString nCounter Data

Description

Negative control genes are provided by nCounter Analyzer which can be used to estimate background noise for each sample.

Usage

## S4 method for signature 'NanoStringSet'
negativeControl(object)
## S4 replacement method for signature 'NanoStringSet,matrix'
negativeControl(object) <- value

Arguments

object	A NanoStringSet object.
value	A matrix with negative control genes.

Details

Each code set in the nCounter Analyzer includes several negatives control genes for which no tranCounterript is expected to be present. We use these spike-in negative control genes to estimate background noise for each sample.

Value

A matrix contain negative control genes

Author(s)

Hong Wang <[e-mail]> chi wang <[e-mail]>

See Also

negativeFactor

Examples

data(NanoStringData)
## obtain negative control genes
negativeControl(NanoStringData)

## assign a matrix
n=ncol(exprs(NanoStringData))
r=nrow(negativeControl(NanoStringData))
negative=matrix(rpois(r*n,10),ncol=n)
negativeControl(NanoStringData)=negative

Shedimus/NanoStringDiff documentation built on Dec. 5, 2019, 1:56 a.m.