Up: Component summary
Up: Component summary
Component
FoldChangeSelects differentially expressed genes using fold change as criterion. This filter does not compute fold changes itself but takes them as input. You can also select stably expressed genes below a fold change threshold. For each sample group present in the log ratio matrix, several result sets are created. Set names are generated using configurable patterns.
| Version | 1.1 |
|---|---|
| Bundle | microarray |
| Categories | DEG |
| Authors | Kristian Ovaska (kristian.ovaska@helsinki.fi) |
| Issue tracker | View/Report issues |
| Requires | R |
| Source files | component.xml FoldChange.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| in | LogMatrix | Mandatory | Log ratio data. |
Outputs| Name | Type | Description |
|---|---|---|
| out | SetList | For each sample group, there are gene lists named fcOver
(overexpressed genes), fcUnder (underexpressed) and fcDeg
(differentially expressed). Note that fcDeg is the union
of fcOver and fcUnder. If parameter stableThreshold is given
a value other than zero, the output will also contain a list named
fcStable (stably expressed genes) for each sample group.
There are also two annotation columns, SampleGroup (contains current
column name in logratio) and Type (contains fcOver/fcUnder/fcDeg/fcStable). |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| nameDeg | string | "%s_fcDeg" | Name of the sets for differentially expressed genes. The pattern %s is expanded to the current sample name in logratio. |
| nameOver | string | "%s_fcOver" | Name of the sets for overexpressed genes. The pattern %s is expanded to the current sample name in logratio. |
| nameStable | string | "%s_fcStable" | Name of the sets for stably expressed genes. The pattern %s is expanded to the current sample name in logratio. |
| nameUnder | string | "%s_fcUnder" | Name of the sets for underexpressed genes. The pattern %s is expanded to the current sample name in logratio. |
| stableThreshold | float | 0 | Fold change threshold (in linear scale) for stable genes. Genes with fold change smaller than the threshold in both directions are considered stably expressed. If the parameter has the value zero, no list of stably expressed genes is included in the results. |
| threshold | float | 4 | Fold change threshold (in linear scale). Genes with fold change greater than or equal to the threshold in either direction are considered differentially expressed. |
Test cases| Test case | Parameters▼ | IN in |
OUT out |
|||
|---|---|---|---|---|---|---|
| case1 | (missing) | in | out | |||
| case2 | properties | in | out | |||
|
threshold=8, |
||||||
| case3-onecolumn | (missing) | in | out | |||