Package Bio :: Package Affy :: Module CelFile
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Module CelFile

source code

Reading information from Affymetrix CEL files version 3 and 4.
Classes [hide private]
  ParserError
  Record
Stores the information in a cel file
Functions [hide private]
 
read(handle)
Reads Affymetrix CEL file and returns Record object.
source code
 
read_v4(f)
Reads Affymetrix CEL file, version 4, and returns a corresponding Record object.
source code
 
read_v3(handle)
Reads Affymetrix CEL file, version 3, and returns a corresponding Record object.
source code
Variables [hide private]
  _modeError = ParserError('You\'re trying to open an Affymetrix...
  __package__ = 'Bio.Affy'
Function Details [hide private]

read(handle)

source code 

Reads Affymetrix CEL file and returns Record object.

CEL files version 3 and 4 are supported, and the parser attempts version detection.

Example Usage:

>>> from Bio.Affy import CelFile
>>> with open("Affy/affy_v4_example.CEL", "rb") as handle:
...     c = CelFile.read(handle)
...
>>> c.version == 4
True

read_v4(f)

source code 

Reads Affymetrix CEL file, version 4, and returns a corresponding Record object.

Most importantly record.intensities correspond to intensities from the CEL file.

record.mask and record.outliers are not set.

Example Usage:

>>> from Bio.Affy import CelFile
>>> with open("Affy/affy_v4_example.CEL", "rb") as handle:
...     c = CelFile.read_v4(handle)
...
>>> c.version == 4
True
>>> print(c.intensities.shape)
(5, 5)

read_v3(handle)

source code 

Reads Affymetrix CEL file, version 3, and returns a corresponding Record object.

Example Usage:

>>> from Bio.Affy import CelFile
>>> with open("Affy/affy_v3_example.CEL", "r") as handle:
...     c = CelFile.read_v3(handle)
...
>>> c.version == 3
True

Variables Details [hide private]

_modeError

Value:
ParserError('You\'re trying to open an Affymetrix v4 CEL file. You hav\
e to use a read binary mode, like this `open(filename "rb")`.',)