spotQuality {arrayQuality} | R Documentation

## Diagnostic plots and comparative boxplots for general hybridization, Spot format

### Description

This component provides qualitative diagnostic plots and quantitative measures for assessing general hybridization quality. All results are displayed in a HTML report. Spot format only.

### Usage

    spotQuality(fnames = NULL, path = ".", galfile = NULL, organism = c("Mm", "Hs"),
    compBoxplot = TRUE, reference = NULL, controlMatrix = controlCode,
    controlId = c("ID"), output = FALSE, resdir = ".", dev= "png", DEBUG = FALSE,...)

### 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 (".").
`galfile` | A "character" string naming the galfile associated with the input files. If galfile = NULL, spotQuality will use the first .gal file available in the 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.
`compBoxplot` | Logical. If set to 'FALSE', only qualitative diagnostic plots will be plotted. gpQuality ouput will be limited to a diagnostic plot by gpr file and a marrayRaw object.
`reference` | A matrix resulting from globalQuality, to be used as reference table to compare slides. If 'NULL', the default table corresponding to organism will be used. See details for more information.
`controlMatrix` | A character matrix of n by 2 columns. The first column contains a few regular expression of spotted probe sequences and the second column contains the corresponding control status.
`controlId` | Character string. Name of the column of the gpr file used to define controls.
`output` | Logical. If 'TRUE', normalized M values corresponding to the input GenePix files and 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 (".").
`dev` | A "character" string naming the graphics device. This will take arguments "png", "jpeg" and "ps" only. By default, dev is set to "png".
`DEBUG` | If 'TRUE', debug statements are printed.
`...` | additional arguments

### Details

agQuality returns 2 plots for each Agilent files passed as argument. The first one is a qualitative diagnostic plot, a quick visual way to assess slide quality. The second one is a comparative boxplot: each quality control measure is compared to the range obtained for a database of 'good' slides used as reference. You can use your own set of references created using `globalQuality` passed in the arguments "reference", or use the reference QC values stored in the datasets `MmReferenceDB` and `HsReferenceDB`. All results and quality scores are gathered in a HTML report. For more details about the QC measures and the plots, please refer to the online manual.

### Value

A list of 2 elements:

`mraw` | A marrayRaw object created from the input files.
`quality` | A matrix containing Quality Control measures for all slides.

### Author(s)

Agnes Paquet

### See Also

`globalQuality`, `qualBoxplot`, `readAgilent`

[Package arrayQuality version 1.60.0 Index]