Up: Component summary
Up: Component summary
Function
MicroarrayReaderReads in expression microarray data produced by feature extraction software. Works with any csv-format feature extraction files, such as produced from Agilent, GenePix, custom or such platforms, or MIAME compliant expression data downloadable from Gene Expression Omnibus.
| Version | 0.7 |
|---|---|
| Bundle | microarray |
| Categories | Data Import |
| Authors | Riku Louhimo (Riku.Louhimo@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Source files | component.xml function.scala |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| data | BinaryFolder | Mandatory | Source file directory. |
| sampleNames | CSV | Mandatory | Sample definitions. Must contain at least column
fileCol which contains filenames in
data folder. |
Outputs| Name | Type | Description |
|---|---|---|
| channel1 | LogMatrix | Sample data. |
| channel2 | LogMatrix | Control data. Empty if analyzing one-channel arrays. |
| sampleAnnotation | CSV | Sample-dependent annotations. See AgilentReader.sampleAnnotation for details. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| controlCol | string | "" | Column in data files for control channel. |
| fileCol | string | (no default) | Column in sampleNames for filenames in data. |
| idCol | string | "" | Column in sampleNames for sample names. |
| probeCol | string | "ProbeName" | Column for probeIds in data. |
| probeFilter | string | "" | Rows in source files matching this Boolean expression are excluded from the result. The expression can refer to any cell value of the current row using column names. Boolean and arithmetic operators and parenthesis as defined in Java are available. For example, "Col1!=0 || (Col2==1 && Col3==1)" removes probes that are either control probes or are saturated on any channel; Col1, Col2 and Col3 must be valid columns in input files. |
| sampleCol | string | (no default) | Column in data files for sample channel. |
| twoChannel | boolean | (no default) | Specifies if data is one or two-channel data. |
Test cases| Test case | Parameters▼ | IN data |
IN sampleNames |
OUT channel1 |
OUT channel2 |
OUT sampleAnnotation |
|---|---|---|---|---|---|---|
| case1 | properties | data | sampleNames | channel1 | channel2 | (missing) |
|
twoChannel = false, |
||||||
| case2 | properties | data | sampleNames | channel1 | channel2 | (missing) |
|
twoChannel = true, |
||||||