maQualityPlots {arrayQuality}R Documentation

Qualitative diagnostic plot for general hybridization


This function generates diagnostic plots for a qualitative assessment of slide quality.


maQualityPlots(mrawObj, headerInfo = "", save = TRUE, dev = "png", col=NULL,
badspotfunction=NULL, controlId = c("ID", "Name"), DEBUG = FALSE, ...)


mrawObj marrayRaw or RGList object representing the slides to be tested.
headerInfo Text to be used as header in the diagnostic plot.
save Logical. If 'TRUE', the plot is saved to a file.
dev A "character" string naming the graphics device. This will take arguments "png", "jpeg" and "ps" only. By default, dev is set to "png".
col Vector of colors to use to describe different categories of spots.
badspotfunction Function to use for bad spots on the array.
controlId Character string. Name of the column of the gpr file used to define controls (or provides the name of the probes).
DEBUG If 'TRUE', debug statements are printed.
... additional arguments


Jean Yang


# Example uses swirl dataset...

[Package arrayQuality version 1.0.7 Index]