Description Details Creating Objects Slots Methods Author(s) See Also
A class describing the content a Chip Description File.
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).
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
)
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.
(Cdf): An accesor function for the
ato,
slot.
(Cdf): A replacement function for
atom
slot.
(Cdf): An accesor function for the
name.levels
slot.
(Cdf): A replacement function for
name.levels
slot.
(Cdf): An accesor function for the
pbase
slot.
(Cdf): A replacement function for
pbase
slot.
(Cdf): An accesor function for the
pbase.levels
slot.
(Cdf): A replacement function for
pbase.levels
slot.
(Cdf): renders information about the Cdf
object in a concise way on stdout.
(Cdf): An accesor function for the
tbase
slot.
(Cdf): A replacement function for
tbase
slot.
(Cdf): An accesor function for the
tbase.levels
slot.
(Cdf): A replacement function for
tbase.levels
slot.
L. Gautier <laurent@cbs.dtu.dk>
read.cdffile
,
make.cdf.env
,
make.cdf.package
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