Cdf-class: Class Cdf

Description

A class describing the content a Chip Description File.

Arguments

Creating Objects

new('Cdf', cdfName = ...., # Object of class character name = ...., # Object of class matrix name.levels = ...., # Object of class character pbase = ...., # Object of class matrix pbase.levels = ...., # Object of class character tbase = ...., # Object of class matrix tbase.levels = ...., # Object of class character atom = ...., # Object of class matrix )

Slots

cdfName:: the CDF name tag. Used to link with the right CEL files
name:: Object of class "matrix" of 'factors' for the gene names corresponding to the probes.
name.levels:: Object of class "character" containing the levels corresponding to name.
pbase:: Object of class "matrix" of pbase levels.
pbase.levels:: Object of class "character" containing the levels corresponding to pbase.
tbase:: Object of class "matrix" of tbase levels.
tbase.levels:: Object of class "character" containing the levels corresponding to tbase.
atom:: Object of class "matrix" of atom or probe numbers.

Methods

atom: (Cdf): An accesor function for the ato, slot.
atom<-: (Cdf): A replacement function for atom slot.
name.levels: (Cdf): An accesor function for the name.levels slot.
name.levels<-: (Cdf): A replacement function for name.levels slot.
pbase: (Cdf): An accesor function for the pbase slot.
pbase<-: (Cdf): A replacement function for pbase slot.
pbase.levels: (Cdf): An accesor function for the pbase.levels slot.
pbase.levels<-: (Cdf): A replacement function for pbase.levels slot.
show: (Cdf): renders information about the Cdf object in a concise way on stdout.
tbase: (Cdf): An accesor function for the tbase slot.
tbase<-: (Cdf): A replacement function for tbase slot.
tbase.levels: (Cdf): An accesor function for the tbase.levels slot.
tbase.levels<-: (Cdf): A replacement function for tbase.levels slot.

Details

The class Cdf was designed to store the content of Affymetrix's Chip Definition Files (CDF). This early class is no longer widely used in the package affy. Environments (called cdfenvs) are preferred to have an efficient mapping between probe set identifiers and indexes (needed to access/subset particular probe intensities). Unless one needs to access every information contained in a CDF file, the cdfenvs will be preferred.

The following comments are only relevant to someone with interest in what is in a CDF file. The name associated to each probe is not unique, it corresponds to the gene name. It is very common to have a name repeated 40 times (20 perfect matches and 20 mismatches). Probes can be grouped by pairs: a perfect match (PM) probe has its mismatch (MM) counterpart. The two probes in a pair differ by one base (usually located in the middle of the sequence). The information relative to this particular base are stored in pbase and tbase. At a given position (x,y), having pbase[x,y] == tbase[x,y] means having a MM while having pbase[x,y] != tbase[x,y] means having a perfect mismatch if and only if one of the bases is A while the other is TRUE, or one is G and the other is C. The function pmormm returns TRUE for PMs and FALSE for MMs.

To know more about the file structure of a CDF file, one has to refer to the parsing code (mostly in C).