Bio.Affy.CelFile module

Reading information from Affymetrix CEL files version 3 and 4.

exception Bio.Affy.CelFile.ParserError(*args)

Bases: ValueError

Affymetrix parser error.

__init__(self, *args)

Initialise class.

class Bio.Affy.CelFile.Record

Bases: object

Stores the information in a cel file.

Example usage:

>>> from Bio.Affy import CelFile
>>> with open("Affy/affy_v3_example.CEL", "r") as handle:
...     c = CelFile.read(handle)
...
>>> print(c.ncols, c.nrows)
5 5
>>> print(c.intensities)
[[   234.    170.  22177.    164.  22104.]
 [   188.    188.  21871.    168.  21883.]
 [   188.    193.  21455.    198.  21300.]
 [   188.    182.  21438.    188.  20945.]
 [   193.  20370.    174.  20605.    168.]]
>>> print(c.stdevs)
[[   24.     34.5  2669.     19.7  3661.2]
 [   29.8    29.8  2795.9    67.9  2792.4]
 [   29.8    88.7  2976.5    62.   2914.5]
 [   29.8    76.2  2759.5    49.2  2762. ]
 [   38.8  2611.8    26.6  2810.7    24.1]]
>>> print(c.npix)
[[25 25 25 25 25]
 [25 25 25 25 25]
 [25 25 25 25 25]
 [25 25 25 25 25]
 [25 25 25 25 25]]
__init__(self)

Initialize class.

Bio.Affy.CelFile.read(handle)

Read Affymetrix CEL file and return 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
Bio.Affy.CelFile.read_v4(f)

Read verion 4 Affymetrix CEL file, returns 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("%i by %i array" % c.intensities.shape)
5 by 5 array
Bio.Affy.CelFile.read_v3(handle)

Read version 3 Affymetrix CEL file, and return 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