globalQuality {arrayQuality} | R Documentation

## 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

    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

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

[Package arrayQuality version 1.12.0 Index]