Up: Component summary
Up: Component summary
Component
TransformationCell fluorescense intensity transformation for FACS data. The user can use the transformation plots to check that the transformation looks correct. Ideally it should make the data look like a blob, if dots are aligned to the zero in either of the axis or are placed below zero would mean that the transformation is not separating the values properly and another transformation should be used.
| Version | 1.0 |
|---|---|
| Bundle | flowand |
| Categories | FlowCytometry |
| Authors | Julia Casado (julia.casado@helsinki.fi) |
| Requires | R ; flowCore (R-bioconductor) ; openCyto (R-bioconductor) |
| Source files | component.xml Transformation.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| in | Array<CSV> | Mandatory | An array of CSV files with all the data for a given experiment. |
Outputs| Name | Type | Description |
|---|---|---|
| out | Array<CSV> | Transformed data in a concatenated CSV file. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| channels | string | "*" | A comma-separated list of channel numbers indicating which columns to transform. Antibody names that match partially the names of the columns. The default is for all. If empty, it will not do any transformation. If parameter 'negate' is true then all channels not in this list are transformed. |
| negate | boolean | false | If true, the transformation will be applied to all channels except those defined in the 'channels' parameter. |
| transformation | string | "arcsinhTransform(transformationId='defaultArcsinhTransform', a=1, b=2)" | The transformation method to apply, open definition of an object of type transform. Examples: linearTransform(transformationId="defaultLinearTransform", a = 1, b = 0) lnTransform(transformationId="defaultLnTransform", r=1, d=1) logicleTransform(transformationId="defaultLogicleTransform", w = 0.5, t = 262144, m = 4.5, a = 0) biexponentialTransform(transformationId="defaultBiexponentialTransform", a = 0.5, b = 1, c = 0.5, d = 1, f = 0, w = 0, tol = .Machine$double.eps^0.25, maxit = as.integer(5000)) arcsinhTransform(transformationId="defaultArcsinhTransform", a=1, b=1, c=0) quadraticTransform(transformationId="defaultQuadraticTransform", a = 1, b = 1, c = 0) logTransform(transformationId="defaultLogTransform", logbase=10, r=1, d=1) scaleTransform(transformationId="defaultScaleTransform", a, b) truncateTransform(transformationId="defaultTruncateTransform", a=1) |
Test cases| Test case | Parameters▼ | IN in |
OUT out |
|---|---|---|---|
| case1 | (missing) | in | out |