basicRMA: Simplified interface to RMA.

In oligo: Preprocessing tools for oligonucleotide arrays

Description

Simple interface to RMA.

Usage

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

Arguments

pmMat	Matrix of intensities to be processed.
pnVec	Probeset names.
normalize	Logical flag: normalize?
background	Logical flag: background adjustment?
bgversion	Version of background correction.
destructive	Logical flag: use destructive methods?
verbose	Logical flag: verbose.
...	Not currently used.

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]

Example output

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

Loading required package: oligoClasses
No methods found in package 'RSQLite' for request: 'dbGetQuery' when loading 'oligoClasses'
Welcome to oligoClasses version 1.38.0
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 object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

================================================================================
Welcome to oligo version 1.40.2
================================================================================
Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'
Background correcting
Normalizing
Calculating Expression
     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

oligo documentation built on Nov. 8, 2020, 6:52 p.m.