RPA.preprocess: RPA preprocessing
In RPA: RPA: Robust Probabilistic Averaging for probe-level analysis

Description Usage Arguments Details Value Author(s) References Examples

Preprocess AffyBatch object for RPA.

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RPA.preprocess(abatch, bg.method = "rma",
  normalization.method = "quantiles.robust", cdf = NULL, cel.files = NULL,
  cel.path = NULL, quantile.basis = NULL)

`abatch`	An AffyBatch object.
`bg.method`	Specify background correction method. See bgcorrect.methods(abatch) for options.
`normalization.method`	Specify normalization method. See normalize.methods(abatch) for options. For memory-efficient online version, use "quantiles.online".
`cdf`	The CDF environment used in the analysis.
`cel.files`	List of CEL files to preprocess.
`cel.path`	Path to CEL file directory.
`quantile.basis`	Optional. Basis for quantile normalization. NOTE: required in original, not log2 scale!

Background correction, quantile normalization and log2-transformation for probe-level raw data in abatch. Then probe-level differential expression is computed between the specified 'reference' array (cind) and the other arrays. Probe-specific variance estimates are robust against the choice of reference array.

fcmat: Probes x arrays preprocessed differential expression matrix. cind: Specifies which array in abatch was selected as a reference in calculating probe-level differential expression. cdf: The CDF environment used in the analysis. set.inds: Indices for probes in each probeset, corresponding to the rows of fcmat.

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:
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  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'