biopython v1.71.0 Bio.Affy.CelFile

Reading information from Affymetrix CEL files version 3 and 4.

Link to this section Summary

Functions

Read Affymetrix CEL file and return Record object

Read version 3 Affymetrix CEL file, and return corresponding Record object

Read verion 4 Affymetrix CEL file, returns corresponding Record object

Link to this section Functions

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

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

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