globalQuality: Quality measures for general hybridization.
In arrayQuality: Assessing array quality on spotted arrays

Description Usage Arguments Value Author(s) See Also Examples

This function provides Quality Control measures for GenePix, Spot and Agilent format files. It is used to create a table of measures to be used as reference in gpQuality, spotQuality or agQuality.

1 2	globalQuality(fnames = NULL, path = ".", organism = c("Mm", "Hs"), output = FALSE, resdir = ".", DEBUG = FALSE, inputsource = "readGPR", controlId="ID",...)

`fnames`	A "character" string naming the input files.
`path`	a "character" string representing the data directory. By default this is set to the current working directory (".").
`organism`	A "character" string naming the organism genome printed on the array, either "Mm" or "Hs". By default, organism is set to "Mm". It is used to retrieve the corresponding reference tables.
`output`	Logical. If 'TRUE', the quality measures are printed to a file.
`resdir`	A "character" string representing the directory where the results will be saved. By default, this is set to the current working directory (".").
`DEBUG`	If 'TRUE', debug statements are printed.
`inputsource`	A "character" string providing the name of the function to use to read the input files. It should be inputsource = "readGPR" for GenePix format files, inputsource = "readSpot" for Spot files, or inputsource = "readAgilent" for Agilent format. By default, 'inputsource' is set to "readGPR".
`controlId`	Character string. Name of the column of the gpr file used to define controls.
`...`	additional arguments

A matrix of Quality Control measures, each column representing a different input slide.

Agnes Paquet

gpQuality, slideQuality, MmReferenceDB, readGPR, readSpot, readAgilent

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datadir <- system.file("gprQCData", package="arrayQuality")
if (interactive())
reference <- globalQuality(fnames="9Mm137.gpr", path=datadir, organism="Mm")