estNormalizationFactors: estimate normalization factors,include positive size factors,...

In NanoStringDiff: Differential Expression Analysis of NanoString nCounter Data

Description

This function estimates positive size factors, background noise and housekeeping size factors for the input "NanoStringSet" object and return the same object with positiveFactor, negativeFactor and housekeepingFactor slots filled or replaced.

Usage

   estNormalizationFactors(NanoStringData)

Arguments

NanoStringData

An object of "NanoStringSet" class.

Value

The same "NanoStringSet" object with positiveFactor, negativeFactor and housekeepingFactor field filled or replaced.

Author(s)

hong wang <[e-mail]> chi wang <[e-mail]>

Examples

data(NanoStringData)
NanoStringData=estNormalizationFactors(NanoStringData)
pf=positiveFactor(NanoStringData)
nf=negativeFactor(NanoStringData)
hf=housekeepingFactor(NanoStringData)

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':

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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

NanoStringDiff documentation built on Nov. 8, 2020, 7:56 p.m.