Up: Component summary
Up: Component summary
Function
AgilentImportImports 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) |
| Issue tracker | View/Report issues |
| 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), |
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| case2_defaults | (missing) | agilentInput | sampleNames | groups | logratio | channels | (missing) | (missing) | (missing) | (missing) |