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)
Issue tracker	View/Report issues
Requires	R
Source files	component.xml ExpressionExtremes.r
Usage	Example with default values ExpressionExtremes( in = LogMatrix, highID = "%s_topMost", highNumber = 100, lowID = "%s_bottomMost", lowNumber = 0 )

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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