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Up: Component summary
Component
IlluminaReaderImports gene expression data from Illumina BeadStudio output files. Use "Sample Probe Profile.txt" files.
The input is a directory of CSV files, each of which represents one Illumina slide. One Illumina slide contains multiple arrays. Input files and arrays used in analysis are defined in a separate CSV file.
The output expr is a matrix containing ProbeIDs and VST (variance stabilizing transform) or log2 transformed intensity values. First column of the output matrix expr is the ProbeID followed by columns each representing one array.
The output probeAnnotation contains annotation columns from input CSV files that do not depend on the sample being processed. The output groups is generated based on sampleNames input.
| Version | 1.1.1 |
|---|---|
| Bundle | microarray |
| Categories | Data Import |
| Authors | Lilli Saarinen (Lilli.Saarinen@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Requires | R ; libxml2-dev (DEB) ; libcurl4-gnutls-dev (DEB) ; lumi (R-bioconductor) |
| Source files | component.xml IlluminaReader.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| illumina | IlluminaDirectory | Mandatory | Illumina source file directory. |
| sampleNames | CSV | Mandatory | Sample definitions. The table contains columns "SampleID" (key), "Filename" (relative to the Illumina source directory), "Description" (sample name). "SampleID" format is [slide code]_[slide position], e.g. 5038690025_B. |
Outputs| Name | Type | Description |
|---|---|---|
| expr | LogMatrix | VST or log2 transformed intensity data, where probe value is the mean of the (~30) bead replicates. |
| probeAnnotation | AnnotationTable | Probe annotations that are not sample-dependent. Annotation columns are specified using probeAnnotation parameter. |
| groups | SampleGroupTable | Sample group table that is generated based on sampleNames. All groups have the type sample. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| convertNuID | boolean | false | Boolean argument indicating either the conversion of nucleotide universal identifier (nuID) is done or not. |
| decimal | string | "," | The character used in the source files for decimal points. |
| probeAnnotation | string | "" | Comma-separated list of column names in input CSV files that contain probe annotation. These are extracted to the probeAnnotation output. If default value is selected, only default annotation columns defined by lumi-package are extracted. (See lumi-package documentation for more information.) |
| transformation | string | "log2" | Type of data transformation. Either log2 (default) or variance stabilizing transform (VST). |
Test cases| Test case | Parameters▼ | IN illumina |
IN sampleNames |
OUT expr |
OUT probeAnnotation |
OUT groups |
|---|---|---|---|---|---|---|
| case1 | properties | illumina | sampleNames | expr | probeAnnotation | groups |
|
probeAnnotation=ProbeID,TargetID,ENTREZ_GENE_ID |
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| case2 | properties | illumina | sampleNames | expr | probeAnnotation | groups |
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| case3 | properties | illumina | sampleNames | expr | probeAnnotation | groups |
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probeAnnotation=ProbeID,TargetID,ENTREZ_GENE_ID |
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| case4_failure | properties | illumina | sampleNames | (expecting failure) | (expecting failure) | (expecting failure) |
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probeAnnotation=ProbeID,TargetID,ENTREZ_GENE_ID |
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