nuseFun: Create an image with boxplots of normalized Unscaled Standard...

In ammar257ammar/ArrayAnalysis-Bioconductor: ArrayAnalysis

Create an image with boxplots of normalized Unscaled Standard Errors (NUSE)

Description

This function (from functions_imagesQC.R) creates an image with boxplots of normalized Unscaled Standard Errors (NUSE) for each array. It calls the NUSE function (affyPLM Bioconductor package). An object obtained by calling fitPLM (affyPLM) is needed. If this object is not provided, it will be computed internally within this function.

Usage

nuseFun(
  Data,
  Data.pset = 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)
Data.pset	(Status: optional, Default:NULL) An object obtained by calling fitPLM (affyPLM), used for each but the raw plot. When not provided, it is computed within the function.(datatype: PLMset)
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 containing boxplots of the NUSE values per array, called "RawDataNUSEplot"

Examples

# By default, the script will call:
# nuseFun(rawData, Data.pset=rawData.pset, experimentFactor, plotColors, legendColors)
# where rawData.pset has been constructed by calling:
# rawData.pset <- fitPLM(rawData)

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