Simplified interface to RMA.

Description

Simple interface to RMA.

Usage

basicRMA(pmMat, pnVec, normalize = TRUE, background = TRUE, bgversion = 2, destructive = FALSE, verbose = TRUE, ...)

Arguments

Value

Matrix.

Examples

set.seed(1)
pms <- 2^matrix(rnorm(1000), nc=20)
colnames(pms) <- paste("sample", 1:20, sep="")
pns <- rep(letters[1:10], each=5)
res <- basicRMA(pms, pns, TRUE, TRUE)
res[, 1:3]

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(oligo)
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, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: oligoClasses
Welcome to oligoClasses version 1.34.0
Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
================================================================================
Welcome to oligo version 1.36.1
================================================================================
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/oligo/basicRMA.Rd_%03d_medium.png", width=480, height=480)
> ### Name: basicRMA
> ### Title: Simplified interface to RMA.
> ### Aliases: basicRMA
> ### Keywords: manip
> 
> ### ** Examples
> 
> set.seed(1)
> pms <- 2^matrix(rnorm(1000), nc=20)
> colnames(pms) <- paste("sample", 1:20, sep="")
> pns <- rep(letters[1:10], each=5)
> res <- basicRMA(pms, pns, TRUE, TRUE)
Background correcting
Normalizing
Calculating Expression
> res[, 1:3]
     sample1      sample2    sample3
a -1.4508069 -1.171727192 -2.5113158
b -1.1815870 -1.574840431  0.3345490
c -1.7335906 -0.991096835 -1.8233019
d -1.1314596 -1.355419255 -1.3873967
e -0.5394549 -2.328551208 -0.9644461
f -1.7314877 -1.532837826 -0.9130684
g -1.6510575 -2.082266169 -1.2910605
h -1.7806949 -0.949080495 -1.9921828
i -1.5998318  0.004118059 -2.6976527
j -1.7892072 -2.447325173 -1.8221758
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>