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MicroarrayReader

Reads in expression microarray data produced by feature extraction software. Works with any csv-format feature extraction files, such as produced from Agilent, GenePix, custom or such platforms, or MIAME compliant expression data downloadable from Gene Expression Omnibus.

Version 0.7
Bundle microarray
Categories Data Import
Authors Riku Louhimo (Riku.Louhimo@Helsinki.FI)
Issue tracker View/Report issues
Source files component.xml function.scala
Usage Example with default values

Inputs

Name Type Mandatory Description
data BinaryFolder Mandatory Source file directory.
sampleNames CSV Mandatory Sample definitions. Must contain at least column fileCol which contains filenames in data folder.

Outputs

Name Type Description
channel1 LogMatrix Sample data.
channel2 LogMatrix Control data. Empty if analyzing one-channel arrays.
sampleAnnotation CSV Sample-dependent annotations. See AgilentReader.sampleAnnotation for details.

Parameters

Name Type Default Description
controlCol string "" Column in data files for control channel.
fileCol string (no default) Column in sampleNames for filenames in data.
idCol string "" Column in sampleNames for sample names.
probeCol string "ProbeName" Column for probeIds in data.
probeFilter string "" Rows in source files matching this Boolean expression are excluded from the result. The expression can refer to any cell value of the current row using column names. Boolean and arithmetic operators and parenthesis as defined in Java are available. For example, "Col1!=0 || (Col2==1 && Col3==1)" removes probes that are either control probes or are saturated on any channel; Col1, Col2 and Col3 must be valid columns in input files.
sampleCol string (no default) Column in data files for sample channel.
twoChannel boolean (no default) Specifies if data is one or two-channel data.

Test cases

Test case Parameters IN
data
IN
sampleNames
OUT
channel1
OUT
channel2
OUT
sampleAnnotation
case1 properties data sampleNames channel1 channel2 (missing)

twoChannel = false,
fileCol = Filename,
sampleCol = channel1,
idCol = SampleID

case2 properties data sampleNames channel1 channel2 (missing)

twoChannel = true,
fileCol = Filename,
sampleCol = channel1,
controlCol = channel2,
idCol = SampleID


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