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