Up: Component summary
Up: Component summary
Component
ACGHnormNormalizes two channel array CGH data with LOESS, median or mode. If median or mode normalization is used, missing values are imputed. Cellular admixture correction of tumor samples has been deprecated.
The component outputs the residuals of the fit (i.e., normalized case channel), the fit curve, and the unchanged control channel. The latter is included to simplify code downstream from ACGHnorm.
| Version | 1.4 |
|---|---|
| Bundle | microarray |
| Categories | Normalization Preprocessing Copy Number Analysis |
| Authors | Riku Louhimo (Riku.Louhimo@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Requires | R ; limma (R-bioconductor) ; CGHcall (R-bioconductor) |
| Source files | component.xml ACGHnorm.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| caseIn | CSV | Mandatory | Probe intensities of the case channel of an Array CGH experiment, preferrably as output by AgilentReader. |
| control | CSV | Mandatory | Probe intensities of the control channel of an Array CGH experiment, preferrably as output by AgilentReader. |
| admixtureMatrix | CSV | Optional | Two column csv containing sample names as first column and the proportion of tumor versus normal cells (i.e., samplewise cell admixture) as the second column. Only used if 'adjustCellularity=true'. Deprecated. |
| probeAnnotation | CSV | Optional | Optional annotation table for expression probes. Must contain columns for 'probeid', 'chr','start' and 'end' the exact values of which are given as parameters. |
Outputs| Name | Type | Description |
|---|---|---|
| casechannel | LogMatrix | Normalized intensities for the case channel (the residuals of the fit). |
| controlchannel | LogMatrix | The control channel matrix. |
| fit | LogMatrix | The fit curve. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| adjustCellularity | boolean | false | Adjust for the cellular admixture of each sample (i.e., proportion of cancer versus normal cells in sample). See admixtureMatrix input. This parameter is only used if method is one of 'median' or 'mode'. Deprecated. |
| chrCol | string | "Chr" | Column name of chromosome annotation. This parameter is only used if method is one of 'median' or 'mode'. |
| endCol | string | "End" | Column name of probe position end locus. This parameter is only used if method is one of 'median' or 'mode'. |
| idCol | string | "" | Column name of probe ids. If not given, assumed to be the first column. This parameter is only used if method is one of 'median' or 'mode'. |
| iterations | int | 4 | Number of iterations of loess fit. Only used if method='loess'. |
| method | string | "loess" | Normalization method to be used. One of 'loess', 'median' or 'mode'. |
| span | float | 0.3 | Numeric parameter between 0 and 1 specifying proportion of data to be used in the local regression moving window. Larger numbers give smoother fits. Only used if method='loess'. |
| startCol | string | "Start" | Column name of probe position start locus. This parameter is only used if method is one of 'median' or 'mode'. |
Test cases| Test case | Parameters▼ | IN caseIn |
IN control |
IN admixtureMatrix |
IN probeAnnotation |
OUT casechannel |
OUT controlchannel |
OUT fit |
|---|---|---|---|---|---|---|---|---|
| case1 | (missing) | caseIn | control | (missing) | (missing) | casechannel | controlchannel | fit |
| case2 | properties | caseIn | control | (missing) | (missing) | casechannel | (missing) | fit |
|
iterations=3, |
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| case3 | properties | caseIn | control | admixtureMatrix | probeAnnotation | casechannel | controlchannel | (missing) |
|
method = median, |
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