readCelHeader: Parsing the header of an Affymetrix CEL file

In HenrikBengtsson/affxparser: Affymetrix File Parsing SDK

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.

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.

Value

A named list with components described below. The entries are obtained from the Fusion SDK interface functions. We try to obtain all relevant information from the file.

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.

Note

Memory usage:the Fusion SDK allocates memory for the entire CEL file, when the file is accessed. The memory footprint of this function will therefore seem to be (rather) large.

Speed: CEL files of version 2 (standard text files) needs to be completely read in order to report the number of outliers and masked features.

Author(s)

James Bullard and Kasper Daniel Hansen

See Also

readCel() for reading in the entire CEL file. That function also returns the header. See affxparserInfo for general comments on the package and the Fusion SDK.

Examples

  # 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)

HenrikBengtsson/affxparser documentation built on Feb. 9, 2024, 3:13 a.m.