Quality metrics for microarray experiments

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Description

Produce an array quality metrics report. This is the main function of the package.

Usage

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arrayQualityMetrics(expressionset,
  outdir = reporttitle,
  force = FALSE,
  do.logtransform = FALSE,
  intgroup = character(0),
  grouprep,
  spatial = TRUE,
  reporttitle = paste("arrayQualityMetrics report for", deparse(substitute(expressionset))),
  ...)

Arguments

expressionset

a Bioconductor microarray dataset container. This can be an object of class ExpressionSet, AffyBatch, NChannelSet, ExpressionSetIllumina, RGList, MAList.

outdir

the name of the directory in which the report is created; a character of length 1.

force

if the directory named by outdir already exists, then, if force is TRUE, the directory is overwritten, otherwise an error is thrown; if the directory does not exist, the value of force is irrelevant; a logical of length 1.

do.logtransform

indicates whether the data should be logarithm transformed before the analysis; a logical of length 1.

intgroup

the name of the sample covariate(s) used to draw a colour side bar next to the heatmap. The first element of intgroup is also used define sample groups in other plots (boxplots, densities). intgroup should be a character vector, and its elements need to match the columns names of phenoData(expressionset). If its length is 0, then the plots are not decorated with sample covariate information.

grouprep

deprecated. Use argument intgroup instead.

spatial

indicates whether spatial plots should be made; a logical of length 1. This can be useful for large arrays (like Affymetrix hgu133Plus2) when CPU time and RAM resources of the machine would be limiting.

reporttitle

title for the report (character of length 1).

...

further arguments that will be passed on to the different module functions.

Details

See the arrayQualityMetrics vignette for examples of this function.

Value

A side effect of the function is the creation of directory named by outdir containing a HTML report QMreport.html and figures. The function also returns a list with R objects containing the report elements for subsequent programmatic processing.

Author(s)

Audrey Kauffmann and Wolfgang Huber.