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]