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

Description Usage Arguments Details Value Author(s) See Also Examples

Description

user-defined housekeeping control genes can be used to estimate housekeeping factors to adjust variation caused by different sample input.

Usage

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

Arguments

object

A NanoStringSet object.

value

A matrix with housekeeping control genes.

Details

NanoString nCounter analyzer also contains probes for a set of species-specific mRNA housekeeping(reference) genes that are not spike-in the system. Nanostring recommends at least three housekeeping genes, but the more that are included, the more accurate the normalization will be. Housekeeping control genes are expected consistent in their expression levels.

Value

A matrix contain housekeeping control genes

Author(s)

Hong Wang <hong.wang@uky.edu> chi wang <chi.wang@uky.edu>

See Also

housekeepingFactor

Examples

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data(NanoStringData)
## obtain housekeeping control genes
housekeepingControl(NanoStringData)

## assign a matrix
n=ncol(exprs(NanoStringData))
r=nrow(housekeepingControl(NanoStringData))
housekeeping=matrix(rpois(r*n,1000),ncol=n)
housekeepingControl(NanoStringData)=housekeeping

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