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IlluminaReader

Imports 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

case2 properties illumina sampleNames expr probeAnnotation groups

case3 properties illumina sampleNames expr probeAnnotation groups

probeAnnotation=ProbeID,TargetID,ENTREZ_GENE_ID

case4_failure properties illumina sampleNames (expecting failure) (expecting failure) (expecting failure)

probeAnnotation=ProbeID,TargetID,ENTREZ_GENE_ID


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