Quality measures for general hybridization.

Description

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.

Usage

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

Arguments

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

Value

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

Author(s)

Agnes Paquet

See Also

gpQuality, slideQuality, MmReferenceDB, readGPR, readSpot, readAgilent

Examples

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

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