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DuplicateQuality

Estimates microarray chip quality by printing expression distributions for duplicate probes. The assumption is that duplicate probes should have similar expression values and high variance indicates quality problems.

The report contains a table for each column in 'expr' that shows distribution parameters for some of the most frequent duplicate probes. Also, there is a spatial plot for each column that contains z-values for all duplicate probes. Z-values are derived with the formula Z = (X-median) / SD, where X is the raw value of the spot in question and median and SD are distribution parameters for the probe class. The figure shows the z-value range from -2 (green) to 2 (red).

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 DuplicateQuality.r
Usage Example with default values

Inputs

Name Type Mandatory Description
expr LogMatrix Mandatory Expression data.
geneAnnotation AnnotationTable Mandatory Must contain the column named by the parameter column. Values from this column are used to detect duplicates. Also must contain the columns Row and Col.

Outputs

Name Type Description
report Latex Quality report.

Parameters

Name Type Default Description
column string "ProbeName" Column name in geneAnnotation that is used to identify duplicate probes. All spots that have the same ID are considered duplicates.

Test cases

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

column=Name


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