readCelHeader: Parsing the header of an Affymetrix CEL file

Description

Reads in the header of an Affymetrix CEL file using the Fusion SDK.

Usage

readCelHeader(filename)

Arguments

filename

the name of the CEL file.

Value

filename: the name of the cel file.
version: the version of the cel file.
cols: the number of columns on the chip.
rows: the number of rows on the chip.
total: the total number of features on the chip. Usually equal to rows times cols, but since it is a separate attribute in the SDK we decided to include it anyway.
algorithm: the algorithm used to create the CEL file.
parameters: the parameters used in the algorithm. Seems to be semi-colon separated.
chiptype: the type of the chip.
header: the entire header of the CEL file. Only available for non-calvin format files.
datheader: the entire dat header of the CEL file. This contains for example a date.
librarypackage: the library package name of the file. Empty for older versions.
cellmargin: a parameter used to generate the CEL file. According to Affymetrix, it designates the number of pixels to ignore around the feature border when calculating the intensity value (the number of pixels ignored are cellmargin divided by 2).
noutliers: the number of features reported as outliers.
nmasked: the number of features reported as masked.

Details

This function returns the header of a CEL file. Affymetrix operates with different versions of this file format. Depending on what version is being read, different information is accessible.

Examples

Run this code

  # Scan current directory for CEL files
  files <- list.files(pattern="[.](c|C)(e|E)(l|L)$")
  if (length(files) > 0) {
    header <- readCelHeader(files[1])
    print(header)
    rm(header)
  }

  # Clean up
  rm(files)