Diagnostic plots and comparative boxplots for general hybridization

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Description

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

Usage

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gpQuality(fnames = NULL, path = ".", organism = c("Mm", "Hs"),
compBoxplot = TRUE, reference = NULL, controlMatrix = controlCode,
controlId = c("ID", "Name"), output = FALSE, resdir = ".", dev= "png",
val=c("maM", "maA"),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 (".").

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. By default, controlMatrix is set to controlCode.

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".

val

A "character" string representing the slotNames to be written in the output file.

DEBUG

If 'TRUE', debug statements are printed.

...

additional arguments

Details

gpQuality returns 2 plots for each GenePix 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 and qualRefTable passed in the arguments "reference" and "scalingTable", or use the reference QC values stored in the datasets MmReferenceDB and MmScalingTable. 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, scaleRefTable

Examples

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

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