backgroundPlot: Create an image of the background intensities and deviations

In ammar257ammar/ArrayAnalysis-Bioconductor: ArrayAnalysis

Create an image of the background intensities and deviations

Description

This function (from functions_imagesQC.R) creates an image of the background intensities and deviations for each array based on the qc (simpleaffy Bioconductor package) function, which generally only work for chiptypes with perfect match and mismatch probes, but even not for all of those. As such, when these statistics are not provided as parameters, trys are used in this function to compute them internally. Values for which the try fails are not computed, but the script will continue after giving a warning.

Usage

backgroundPlot(
  Data,
  quality = NULL,
  experimentFactor = NULL,
  plotColors = NULL,
  legendColors = NULL,
  WIDTH = 1000,
  HEIGHT = 1414,
  POINTSIZE = 24,
  MAXARRAY = 41
)

Arguments

Data	(Status: required) The raw data object (datatype: AffyBatch)
quality	(Status: optional, Default:NULL) object obtained by calling the qc function (simpleaffy).When not provided, it is computed within the function.(datatype: QCStats)
experimentFactor	(Status: required, Default:NULL) The factor of groups. (datatype: factor)
plotColors	(Status: required, Default:NULL) Vector of colors assigned to each array. (datatype: character)
legendColors	(Status: required, Default:NULL) Vector of colors assigned to each experimental group. (datatype: character)
WIDTH	(Status: optional, Default:1000) png image width (datatype: number)
HEIGHT	(Status: optional, Default:1414) png image height (datatype: number)
POINTSIZE	(Status: optional, Default:24) png image point size (datatype: number)
MAXARRAY	(Status: optional, Default:41) threshold to adapt the image to the number of arrays (datatype: number)

Value

A PNG image of background intensities, called "RawDataBackgroundPlot"

Examples

# backgroundPlot(rawData, quality=quality, experimentFactor, plotColors,legendColors)

ammar257ammar/ArrayAnalysis-Bioconductor documentation built on Jan. 29, 2024, 7:21 a.m.