Up: Component summary
Up: Component summary
Component
IlluminaPlotProduces 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 |
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|---|---|---|---|---|---|---|
| case1 | properties | in | out | |||
|
plotType=boxplot, |
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| case2_failure | properties | in | (expecting failure) | |||
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plotType= |
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