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SpatialContrast

Finds two spatial regions in expression data that have a maximum contrast in average expression value. The regions correspond to the lowest and highest expression regions on the chip.

Version 1.0
Bundle microarray
Categories Quality Control
Authors Kristian Ovaska (kristian.ovaska@helsinki.fi)
Issue tracker View/Report issues
Requires R
Source files component.xml SpatialContrast.r
Usage Example with default values

Inputs

Name Type Mandatory Description
expr LogMatrix Mandatory Expression data.
geneAnnotation AnnotationTable Mandatory Contains location information for the probes in columns 'Row' and 'Col'.

Outputs

Name Type Description
report Latex Spatial region report.

Parameters

Name Type Default Description
margin int 0 Number of probes on each side (left, upper, right, lower) that are left out of the analysis.
regionArea float 1000 The regions must contain at least this many probes.

Test cases

Test case Parameters IN
expr
IN
geneAnnotation
OUT
report
case1 properties expr geneAnnotation report

regionArea=16

case2 properties expr geneAnnotation report

regionArea=9,
margin=1


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