arrayQualityMetrics {arrayQualityMetrics}R Documentation

Quality metrics on microarray experiments

Description

arrayQualityMetrics performs quality metrics on ExpressionSet, AffyBatch or NChannelSet 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, split.plots)

arrayQualityMetrics(expressionset,
                    outdir = getwd(),
                    force = FALSE,
                    do.logtransform = FALSE,
                    split.plots = FALSE)

## S4 method for signature 'AffyBatch':
arrayQualityMetrics(expressionset, outdir, force, do.logtransform, split.plots)
## S4 method for signature 'NChannelSet':
arrayQualityMetrics(expressionset, outdir, force, do.logtransform, split.plots)

Arguments

expressionset is an object of class ExpressionSet, AffyBatch or NChannelSet.
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.
split.plots If the number of studied array is more than 50 it is adviced to define a number of experiments to represent on the density plots.

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>

Examples

  ## Not run: 
    library(ALLMLL)
    data(MLL.A)
    arrayQualityMetrics(expressionset = MLL.A,
                        outdir ="MLL",
                        do.logtransform = TRUE,
                        split.plots = 10)
    # "MLL_QMreport.html" is a report created in the working directory
    # on the logarithm expression data of the MLL.A AffyBatch.
    # 10 experiments are represented by density plots.
    
## End(Not run)

[Package arrayQualityMetrics version 1.2.1 Index]