get.probe.matrix: get.probe.matrix
In RPA: RPA: Robust Probabilistic Averaging for probe-level analysis

Description Usage Arguments Details Author(s) References Examples

Get probe matrix.

1 2	get.probe.matrix(cels, cdf = NULL, quantile.basis, bg.method = "rma", normalization.method = "quantiles", batch = NULL, verbose = TRUE)

`cels`	List of CEL files to preprocess
`cdf`	Specify an alternative CDF environment
`quantile.basis`	Pre-calculated basis for quantile normalization in log2 domain
`bg.method`	Specify background correction method. See bgcorrect.methods() for options.
`normalization.method`	normalization method
`batch`	batch
`verbose`	Print progress information during computation

Returns background-corrected, quantile normalized log2 probes x samples matrix

Leo Lahti leo.lahti@iki.fi

See citation("RPA")

Loading required package: affy
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: 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: phyloseq

Attaching package: 'phyloseq'

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

    sampleNames

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

    sampleNames


RPA Copyright (C) 2008-2016 Leo Lahti.
This program comes with ABSOLUTELY NO WARRANTY.
This is free software, and you are welcome to redistribute it under the FreeBSD open source license.

Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'