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IlluminaPlot

Produces quality control plots. The quality control plots include density plot, box plot, pairwise scatter plot between microarrays, pairwise MA-plot between microarrays and sample relations (hierarchical clustering).

The input is a matrix containing ProbeIDs and raw or normalized intensity values at log2 scale. First column of the input is the ProbeID followed by columns each representing one array.

In density plot, box plot and sample relations plot all samples are plotted on the same figure. In pairwise scatter plot and MA-plot max 4 and min 2 samples are plotted on the same figure.

Example plot: boxplot.

Version 1.1
Bundle microarray
Categories Latex Plot
Authors Lilli Saarinen (Lilli.Saarinen@Helsinki.FI)
Issue tracker View/Report issues
Requires R ; libxml2-dev (DEB) ; libcurl4-gnutls-dev (DEB) ; lumi (R-bioconductor) ; beadarray (R-bioconductor)
Source files component.xml IlluminaPlot.r
Usage Example with default values

Inputs

Name Type Mandatory Description
in LogMatrix Mandatory Input matrix of data.

Outputs

Name Type Description
out Latex Plot

Parameters

Name Type Default Description
height float 11 Height of each plot in cm.
plotType string (no default) Comma-separated list of plots, e.g. "density,boxplot,pair". density = density plot; boxplot = box plot; pair = scatter plot; MAplot = MA-plot; sampleRelation = sample relations (hierarchical clustering).
sectionTitle string "QC plots" Section title.
width float 14 Width of each plot in cm.

Test cases

Test case Parameters IN
in
OUT
out
case1 properties in out

plotType=boxplot,
sectionTitle = Quality Control plots,
width=10,
height=12

case2_failure properties in (expecting failure)

plotType=


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