Up: Component summary
Up: Component summary
Component
IlluminaNormalizationPerforms between array normalization for an input matrix. Normalization methods are quantile, ssn (simple scaling normalization), rsn (robust spline normalization), loess, rank invariant and vsn (variance stabilizing normalization). vsn should be directly applied to the raw data, not to the log2/vst transformed data.
The input is a matrix containing ProbeIDs and log2/vst transformed intensity values. First column of the input is the ProbeID followed by columns each representing one array.
The output is a matrix containing ProbeIDs and normalized intensity values. First column of the output is the ProbeID followed by columns each representing one array.
| Version | 1.0 |
|---|---|
| Bundle | microarray |
| Categories | Normalization |
| 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 IlluminaNormalization.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| in | LogMatrix | Mandatory | Input matrix of raw data. |
Outputs| Name | Type | Description |
|---|---|---|
| out | LogMatrix | Output matrix of normalized data. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| method | string | "quantile" | Possible values are "quantile", "ssn", "rsn", "loess", "rankinvariant" and "vsn" normalizations. |
Test cases| Test case | Parameters▼ | IN in |
OUT out |
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|---|---|---|---|---|---|---|
| case1 | properties | in | out | |||
|
method=quantile |
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| case2 | properties | in | out | |||
|
method=loess |
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