arrayQualityMetrics {arrayQualityMetrics}R Documentation

Quality metrics on microarray experiments

Description

arrayQualityMetrics performs quality metrics on ExpressionSet, AffyBatch , NChannelSet, BeadLevelList, RGList, MAList, aqmInputObj, marrayRaw or marrayNorm containing microarray data from any platforms, one or two channels. The results, presented in a HTML report, are designated to allow the user to rapidly assess the quality of a set of arrays.

Usage

## S4 method for signature 'ExpressionSet':
arrayQualityMetrics(expressionset, outdir,
force, do.logtransform, intgroup, grouprep)

arrayQualityMetrics(expressionset,
                    outdir = getwd(),
                    force = FALSE,
                    do.logtransform = FALSE,
                    intgroup = "Covariate",
                    grouprep = FALSE)

## S4 method for signature 'AffyBatch':
arrayQualityMetrics(expressionset, outdir, force,
do.logtransform, intgroup, grouprep)
## S4 method for signature 'NChannelSet':
arrayQualityMetrics(expressionset, outdir,
force, do.logtransform, intgroup, grouprep)
## S4 method for signature 'BeadLevelList':
arrayQualityMetrics(expressionset, outdir,
force, do.logtransform, intgroup, grouprep)
## S4 method for signature 'RGList':
arrayQualityMetrics(expressionset, outdir,
force, do.logtransform, intgroup, grouprep)
## S4 method for signature 'MAList':
arrayQualityMetrics(expressionset, outdir,
force, do.logtransform, intgroup, grouprep)
## S4 method for signature 'aqmInputObj':
arrayQualityMetrics(expressionset, outdir,
force, do.logtransform, intgroup, grouprep)
## S4 method for signature 'marrayRaw':
arrayQualityMetrics(expressionset, outdir,
force, do.logtransform, intgroup, grouprep)
## S4 method for signature 'marrayNorm':
arrayQualityMetrics(expressionset, outdir,
force, do.logtransform, intgroup, grouprep)

Arguments

expressionset is an object of class ExpressionSet, AffyBatch , NChannelSet , BeadLevelList , RGList , MAList , aqmInputObj , marrayRaw or marrayNorm .
outdir is the name of the directory in which the results are created.
force if TRUE, outdir will be overwritten if it already exists.
do.logtransform If TRUE, the data are log transformed before the analysis.
intgroup Name of the column of the phenoData to be used to draw a colour side bar next to the heatmap.
grouprep Decide if you want the boxplots and density plots to be coloured function of the groups set by 'intgroup'. The default is FALSE meaning that the boxplot and density plots will not be represented function of the groups of 'intgroup'.

Details

See the arrayQualityMetrics Vignette for examples of this function.

Value

A directory outdir containing a HTML report named QMreport.html and all the PNG and PDF plots is created.

Author(s)

Audrey Kauffmann, Wolfgang Huber. Maintainer: <audrey@ebi.ac.uk>


[Package arrayQualityMetrics version 2.2.3 Index]