Up: Component summary Function

AgilentImport

Imports Agilent microarray data, merges duplicate probes and creates a log ratio matrix. Optionally, creates a quality control report that contains the following sections: MA plots (see Plot2D); box plots (see BoxPlot); cumulative sum plot (see Plot2D); spatial plots (see SpatialPlot); clustering report (see ClusterReport); correlation report (see CorrelationReport).

Version 1.0
Bundle microarray
Categories Data Import
Authors Kristian Ovaska (kristian.ovaska@helsinki.fi)
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Source files component.xml function.scala
Usage Example with default values

Inputs

Name Type Mandatory Description
agilentInput AgilentDirectory Mandatory Agilent source file directory.
sampleNames CSV Mandatory Sample definitions. The table contains the columns GreenSampleID (sample ID for the sample on green channel), GreenDescription (human-readable description for the sample), RedSampleID, RedDescription, Filename (key; relative to the Agilent source directory).
groups SampleGroupTable Mandatory Log ratio groups. There should be one ratio group for each microarray that converts the green and red channels into log ratios.

Outputs

Name Type Description
logratio LogMatrix Normalized log ratios computed from channel values based on logratioGroups. Control probes have been filtered out and probes with multiple spots have been combined.
channels LogMatrix Normalized green and red channel value in one matrix. Control probes have been filtered out and probes with multiple spots have been combined.
probeAnnotation AnnotationTable Probe annotations that are not sample-dependent. See AgilentReader.portAnnotation for details.
sampleAnnotation CSV Sample-dependent annotations. See AgilentReader.sampleAnnotation for details.
groups SampleGroupTable Sample group table that is generated based on sampleNames. All groups have the type sample.
qcReport Latex Contains subsections for MA plots and duplicate quality report.

Parameters

Name Type Default Description
filterLowQuantile float 0 Quantile between 0 and 1 that is used to filter low intensity probes. If non-zero, probe values below the given quantile are set to NA and probes that are below the quantile in all samples are removed.
probeFilter string "ControlType!=0 || gIsSaturated==1 || rIsSaturated==1 || gIsWellAboveBG==0 || rIsWellAboveBG==0 || gIsFeatPopnOL==1 || rIsFeatPopnOL==1 || gIsBGPopnOL==1 || rIsBGPopnOL==1" Probe filter expression. Corresponds to the filter parameter of AgilentReader.
qualityControl boolean true If true, create quality control plots and include them in the qcReport output. If false, qcReport will be empty.
spatialHighQuantile float 0.95 For spatial quality control plots, this gives the quantile that determines the contrast of the images in the high intensity end. See SpatialPlot.highQuantile for details.
spatialLowQuantile float 0.05 For spatial quality control plots, this gives the quantile that determines the contrast of the images in the low intensity end. See SpatialPlot.lowQuantile for details.

Test cases

Test case Parameters IN
agilentInput
IN
sampleNames
IN
groups
OUT
logratio
OUT
channels
OUT
probeAnnotation
OUT
sampleAnnotation
OUT
groups
OUT
qcReport
case1 properties agilentInput sampleNames groups logratio channels (missing) (missing) (missing) (missing)

probeFilter=ControlType!=0 || (gIsSaturated==1 && rIsSaturated==1),
filterLowQuantile=0.04

case2_defaults (missing) agilentInput sampleNames groups logratio channels (missing) (missing) (missing) (missing)

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