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

In NanoStringDiff: Differential Expression Analysis of NanoString nCounter Data

Description

Negative size factors can be used to adjust background niose for each sample.

Usage

## S4 method for signature 'NanoStringSet'
negativeFactor(object)
## S4 replacement method for signature 'NanoStringSet,numeric'
negativeFactor(object) <- value

Arguments

object	A NanoStringSet object.
value	A vector of background noise.

Details

Accurate estimation of system background is essential for DE detection analysis. 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 vector contain background noise

Author(s)

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

See Also

negativeControl

Examples

data(NanoStringData)
## obtain negative factors
negativeFactor(NanoStringData)

## assign a vector
n=ncol(exprs(NanoStringData))
lamda=rpois(n,10)
negativeFactor(NanoStringData)=lamda

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

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    'browseVignettes()'. To cite Bioconductor, see
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NanoStringDiff documentation built on Nov. 8, 2020, 7:56 p.m.