arrayQualityMetrics: Quality metrics for microarray experiments
In arrayQualityMetrics: Quality metrics report for microarray data sets

Description Usage Arguments Details Value Author(s)

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

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

`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`.

See the arrayQualityMetrics vignette for examples of this function.

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.

Audrey Kauffmann and Wolfgang Huber.

arrayQualityMetrics documentation built on Nov. 8, 2020, 5:18 p.m.