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ExpressionExtremes

Selects differentially expressed genes using expression values as criterion. This component returns N most higly expressed genes (set type: topMost) and M most lowly expressed genes (set type: bottomMost).

Version 1.3
Bundle microarray
Categories DEG
Authors Marko Laakso (Marko.Laakso@Helsinki.FI), Kristian Ovaska (kristian.ovaska@helsinki.fi)
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Requires R
Source files component.xml ExpressionExtremes.r
Usage Example with default values

Inputs

Name Type Mandatory Description
in LogMatrix Mandatory Expression data. Can be single channel or log ratio data.

Outputs

Name Type Description
out SetList List of genes with the highest expression levels. There are two annotation columns, SampleGroup (gives the column name in expr) and Type (topMost/bottomMost).

Parameters

Name Type Default Description
highID string "%s_topMost" Name of the sets for most highly expessed genes. The pattern %s is expanded to the current column name in expr.
highNumber int 100 Number of highly expressed genes to be chosen.
lowID string "%s_bottomMost" Name of the sets for most lowly expessed genes. The pattern %s is expanded to the current column name in expr.
lowNumber int 0 Number of lowly expressed genes to be chosen.

Test cases

Test case Parameters IN
in
OUT
out
case1 (missing) in out
case2 properties in out

highNumber=2,
lowNumber=4

case3_weights properties in out

highNumber=2,
lowNumber=4

case4_list_id properties in out

highNumber=3,
highID=%s_myHighID,
lowID=%s_myLowID


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