pdInfo2Cdf: Generates an Affymetrix CDF file from a Platform Design (PD)...

In aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

Generates an Affymetrix CDF file from a Platform Design (PD) package and a auxiliary CEL file for the same chip type

Description

Generates an Affymetrix CDF file from a Platform Design (PD) package and a auxiliary CEL file for the same chip type. Platform Design (PD) packages are also known as "pdInfo" packages.

Disclaimer: This is a user-contributed function.

Instead of using this method, we recommend to use writeCdf() for the AffyGenePDInfo class.

Usage

pdInfo2Cdf(pdpkg, celfile, overwrite=FALSE, verbose=TRUE, ...)

Arguments

pdpkg	A character string for an existing PD package.
celfile	The pathname to an auxiliary CEL for the same chip type.
overwrite	If TRUE, an existing CDF is overwritten, otherwise an exception is thrown.
verbose	A logical or Verbose.
...	Not used.

Value

Returns (invisibly) the pathname to CDF written. The CDF filename is generated from the name of the PD package.

Limitations

The information available in the PD package is limited and does not contain all information needed to populate a CDF file. In order to workaround these limitations, certain CDF entries are set to predefined/hardwired values. The 'pbase' and 'tbase' entries of the generated CDF file is hardwired to "T" and "A", respectively. Likewise, the 'groupdirection' entry is hardwired to "sense".

Author(s)

Maintained by Mark Robinson. Original code by Samuel Wuest. Code improvements by Henrik Bengtsson.

See Also

Instead of using this method, we recommend to use writeCdf() for the AffyGenePDInfo class.

aroma.affymetrix documentation built on May 29, 2024, 4:32 a.m.