arrayQualityMetrics {arrayQualityMetrics} | R Documentation |
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 |
outdir |
the name of the directory in which the report is created; a character of length 1. |
force |
if the directory named by |
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
|
grouprep |
deprecated. Use argument |
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
|
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.