Collaboration diagram for broad.pda.differentialExpression.RunDifferentialExpression:

Public Member Functions
MatrixWithHeaders	getResults ()

void	writeResults (String outFile) throws IOException

	RunDifferentialExpression (File gctFile, File experimentInfoFile, File chipFile, String save, boolean preprocess, double alpha, int perm) throws IOException, ParseException

	RunDifferentialExpression (MatrixWithHeaders data, Collection< String > group1, Collection< String > group2, int numPerm, double alpha)

	RunDifferentialExpression (MatrixWithHeaders data, Map< String, Collection< String >> groups, int numPerm, double alpha) throws IOException

MatrixWithHeaders	getGenesPassingFDR (double alpha)

MatrixWithHeaders	getFDR ()

Static Public Member Functions
static void	main (String[] args) throws IOException, ParseException

Constructor & Destructor Documentation

broad.pda.differentialExpression.RunDifferentialExpression.RunDifferentialExpression	(	File	gctFile,
		File	experimentInfoFile,
		File	chipFile,
		String	save,
		boolean	preprocess,
		double	alpha,
		int	perm
	)		throws IOException, ParseException

Here is the caller graph for this function:

broad.pda.differentialExpression.RunDifferentialExpression.RunDifferentialExpression	(	MatrixWithHeaders	data,
		Collection< String >	group1,
		Collection< String >	group2,
		int	numPerm,
		double	alpha
	)

Parameters

data	Data set in which to find differentially expressed genes
group1	The list of samples (columns in the data matrix) of group 1
group2	The list of samples (columns in the data matrix) of group 2
numPerm	Number of permutations to perform. Specify 0 to perform the maximal number of permutations
alpha	Significance level

Exceptions

IOException

broad.pda.differentialExpression.RunDifferentialExpression.RunDifferentialExpression	(	MatrixWithHeaders	data,
		Map< String, Collection< String >>	groups,
		int	numPerm,
		double	alpha
	)		throws IOException

Member Function Documentation

MatrixWithHeaders broad.pda.differentialExpression.RunDifferentialExpression.getFDR ( )

MatrixWithHeaders broad.pda.differentialExpression.RunDifferentialExpression.getGenesPassingFDR ( double alpha )

Here is the call graph for this function:

MatrixWithHeaders broad.pda.differentialExpression.RunDifferentialExpression.getResults ( )

static void broad.pda.differentialExpression.RunDifferentialExpression.main ( String[] args ) throws IOException, ParseException

static

Here is the call graph for this function:

void broad.pda.differentialExpression.RunDifferentialExpression.writeResults ( String outFile ) throws IOException

The documentation for this class was generated from the following file: