Component: AffyReader

AffyReader

Imports gene expression or exon array data from Affymetrix CEL-files. CEL-files are recognized by the suffix 'CEL'.

Version	1.1.2
Bundle	microarray
Categories	Data Import Affy
Authors	Marko Laakso (Marko.Laakso@Helsinki.FI), Kari Nousiainen (Kari.Nousiainen@Helsinki.FI), Ping Chen (ping.chen@helsinki.fi)
Issue tracker	View/Report issues
Requires	R ; affy (R-bioconductor) ; affydata (R-bioconductor) ; gcrma (R-bioconductor) ; plier (R-bioconductor) ; aroma.affymetrix (R-package) ; affxparser (R-bioconductor) ; AffymetrixDataTestFiles (R-bioconductor)
Source files	component.xml AffyReader.r
Usage	Example with default values AffyReader( affy = AffyDirectory, sampleNames = CSV, acceptCELOnly = true, arrayType = <string>, cdf = <string>, idType = "AffyProbeSet", metaData = "", normalizationMethod = "rma", quantileNormalization = true, skipCELFiles = false, suffixLength = 0 )

Version

1.1.2

Bundle

microarray

Categories

Data Import Affy

Authors

Marko Laakso (Marko.Laakso@Helsinki.FI), Kari Nousiainen (Kari.Nousiainen@Helsinki.FI), Ping Chen (ping.chen@helsinki.fi)

Issue tracker

View/Report issues

Requires

R ; affy (R-bioconductor) ; affydata (R-bioconductor) ; gcrma (R-bioconductor) ; plier (R-bioconductor) ; aroma.affymetrix (R-package) ; affxparser (R-bioconductor) ; AffymetrixDataTestFiles (R-bioconductor)

Source files

component.xml AffyReader.r

Usage

Example with default values

Inputs

Name	Type	Mandatory	Description
affy	AffyDirectory	Mandatory	Affymetrix source file directory.
sampleNames	CSV	Mandatory	Sample definitions. The table contains columns "SampleID" (key), "Filename" (relative to the Affy source directory), "Description". If some samples are not found in the source file directory, they are ignored.

Name

Type

Mandatory

Description

affy

AffyDirectory

Mandatory

Affymetrix source file directory.

sampleNames

CSV

Mandatory

Sample definitions. The table contains columns "SampleID" (key), "Filename" (relative to the Affy source directory), "Description". If some samples are not found in the source file directory, they are ignored.

Outputs

Name	Type	Description
expr	LogMatrix	Normalized gene expression matrix. Expression values are in log base 2 scale.
exprRaw	LogMatrix	Raw, unnormalized gene expression matrix. Notice that expr and exprRaw usually have different number of rows.
groups	SampleGroupTable	Sample group definitions. They are automatically generated based on sampleNames.

Name

Type

Description

expr

LogMatrix

Normalized gene expression matrix. Expression values are in log base 2 scale.

exprRaw

LogMatrix

Raw, unnormalized gene expression matrix. Notice that expr and exprRaw usually have different number of rows.

groups

SampleGroupTable

Sample group definitions. They are automatically generated based on sampleNames.

Parameters

Name	Type	Default	Description
acceptCELOnly	boolean	true	If true, reads only files with .CEL extension, if false, accepts all file extensions.
arrayType	string	(no default)	A string specifying the type of arrays to read. The type is either 'geneArray' or 'exonArray'.
cdf	string	(no default)	Chip annotation file as defined in Bioconductor. For exon array, you should use 'exon.pmcdf' as cdf when 'normalizationMethod' is 'rma' or 'plier'; use 'HuEx-1_0-st-v2' when 'normalizationMethod' is 'firma'.
idType	string	"AffyProbeSet"	Probe set annotation type that is used as a column name for the identifiers of the output file.
metaData	string	""	The directory for storing metadata when 'normalizationMethod' is set to 'firma'. Otherwise, it is not needed.
normalizationMethod	string	"rma"	For gene expression array, normalization could be one of the following normalization methods "rma", "gcrma", "mas5", "dChip" or "plier". For exon array, normalization is 'rma', 'firma' or 'plier'.
quantileNormalization	boolean	true	Boolean argument indicating either the quantile normalization is in use or not. Used by algorithms rma and plier.
skipCELFiles	boolean	false	If true, CEL-files found in the soure file directory but not defined in the sample definition file are skipped. If false, any CEL-files not defined in the sample definition file found in the soure file directory cause an error.
suffixLength	int	0	Character lenght of the gene ID suffix to be removed. This is only used for gene expression array.

Name

Type

Default

Description

acceptCELOnly

boolean

true

If true, reads only files with .CEL extension, if false, accepts all file extensions.

arrayType

string

(no default)

A string specifying the type of arrays to read. The type is either 'geneArray' or 'exonArray'.

cdf

string

(no default)

Chip annotation file as defined in Bioconductor. For exon array, you should use 'exon.pmcdf' as cdf when 'normalizationMethod' is 'rma' or 'plier'; use 'HuEx-1_0-st-v2' when 'normalizationMethod' is 'firma'.

idType

string

"AffyProbeSet"

Probe set annotation type that is used as a column name for the identifiers of the output file.

metaData

string

The directory for storing metadata when 'normalizationMethod' is set to 'firma'. Otherwise, it is not needed.

normalizationMethod

string

"rma"

For gene expression array, normalization could be one of the following normalization methods "rma", "gcrma", "mas5", "dChip" or "plier". For exon array, normalization is 'rma', 'firma' or 'plier'.

quantileNormalization

boolean

true

Boolean argument indicating either the quantile normalization is in use or not. Used by algorithms rma and plier.

skipCELFiles

boolean

false

If true, CEL-files found in the soure file directory but not defined in the sample definition file are skipped. If false, any CEL-files not defined in the sample definition file found in the soure file directory cause an error.

suffixLength

int

Character lenght of the gene ID suffix to be removed. This is only used for gene expression array.

Test cases