Up: Component summary Function

ExpressionImport

Reads expression data, applies all available normalization methods and returns a record with normalized datasets. Normalization is done for the whole table at once. When a two channel array is used, it returns logratio from the two channels. In this case, normalization is applied to the logtatio values.

Version 0.1
Bundle microarray
Categories Data Import
Authors Sirkku Karinen (sirkku.karinen@helsinki.fi)
Issue tracker View/Report issues
Source files component.xml function.scala
Usage Example with default values

Inputs

Name Type Mandatory Description
datasets BinaryFolder Mandatory Foldes that contains the raw expression data files.
sampleNames CSV Mandatory File that specifies the sample names and the corresponding input file in datasets folder.

Outputs

Name Type Description
expr Array<CSV> Array of expression matricies. Each array element (that is expression a matrix) is processed with different normalization method and indexed with the normalization name. Normalization methods for each expression data type is given in constants.and

Parameters

Name Type Default Description
arrayType string (no default) affy = Affymetrics expression expression array,
illumina = Illumina expression expression array,
agilent1CH = Agilent 1 channel expression array,
agilent2CH = Agilent 2 channel expression array,
custom1CH = Agilent 1 channel expression array,
custom2CH = Agilent 2 channel expression array
controlCHCol string "F635 Mean" This is ignored for illumina, affy and one channel array types
includeConstants string "doc-files/constants.and" The file that has the constants for the normalization methods etc.
logratio boolean true In two channel array return is logratio or experession values. If return is expression, samples are named Sample and Sample_ref.
probeCol string "ProbeName" Column name for the probes. Used for custom/agilent arrays.
sampleCHCol string "B532 Mean" This is ignored for illumina or affy array types
sampleFileColumn string "FileName" Column name for file names in sampleNames input
sampleIDColumn string "SampleID" Column name for sample IDs in sampleNames input
series string "" Affymetrix array type.

Test cases

Test case Parameters IN
datasets
IN
sampleNames
OUT
expr
case1_illumina properties datasets sampleNames (missing)

arrayType=illumina,
includeConstants=doc-files/testcase1-constants.and,
sampleFileColumn=Filename

case2_affy properties datasets sampleNames (missing)

arrayType=affy,
series=HG-U133A

case3_oneCh properties datasets sampleNames expr

arrayType=custom1CH,
sampleCHCol=gProcessedSignal,
probeCol=ProbeNames

case4_twoCh properties datasets sampleNames (missing)

arrayType=agilent2CH,
sampleCHCol=gProcessedSignal,
controlCHCol=rProcessedSignal


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