Up: Component summary Component

FoldChange

Selects 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,
stableThreshold=3

case3-onecolumn (missing) in out

Generated 2018-12-16 07:42:09 by Anduril 2.0.0