plotArrayLayout: Create an image of the layout of the current chiptype

In ammar257ammar/ArrayAnalysis-Bioconductor: ArrayAnalysis

Create an image of the layout of the current chiptype

Description

This function (from functions_imagesQC.R) creates an image of the layout of the current chiptype. Thus, this plot does not plot any data, but shows where control and regular perfect match (PM) and (if applicable) mismatch (MM) probes are present on the array. Note: due to resolution issues, banding may seem different from the real situation, e.g. normally on classical chiptypes, PM and MM are present in alternate lines, but patterns may appear due to image resolution. This function tries to load annotation libraries, depending on the chiptype.

Usage

plotArrayLayout(
  Data,
  aType = NULL,
  WIDTH = 1000,
  HEIGHT = 1414,
  POINTSIZE = 24
)

Arguments

Data	(Status: required) The raw data object (datatype: AffyBatch or ExpressionSet)
aType	(Status: optional, Default:NULL) String indicating the type of the current chip, either “PMMM” for chips with perfect match and mismatch probes, or “PMonly” for chips with perfect match probes only. Required when Data is a raw data object. (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)

Value

A PNG image of the expression profiles of the affx controls, called "Array_layout_plot"

Examples

# plotArrayLayout(rawData,aType)

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