NanoStringDataNormalization: Normalize NanoStringData

In NanoStringDiff: Differential Expression Analysis of NanoString nCounter Data

Description

This function is used to get Normalized NanoString Data after adjusting for positive size factors, background noise and housekeeping size factors. Note that the normalized data values should only be used for data exploration / visualization purposes, e.g. drawing a heatmap. To perform differential expression analysis, we recommend users to follow the procedure described in the package vignette.

Usage

   NanoStringDataNormalization(path=path, header=TRUE, designs)

Arguments

path	the path of the file which the data are to be read from.
header	a logical value indicating whether the file contains the names of the variables as its first line. If missing, the value is determined from the file format: header is set to TRUE if and only if the first row contains one fewer field than the number of columns.
designs	a data frame in which the length of vector matches the column number of NanoStringData

Author(s)

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

Examples

##path="/Users/NanoStringdiff-Rcode/Data/horbinski.csv"
##designs=data.frame(control=c(0,0,0,1,1,1))
##NanoStringDataNormalization(path=path, header=TRUE, designs)

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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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.