Perform a full PUMA analysis

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Description

Full analysis including pumaPCA and mmgmos/pumaDE vs rma/limma comparison

Usage

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pumaFull (
	ExpressionFeatureSet = NULL
,	data_dir = getwd()
,	load_ExpressionFeatureSet = FALSE
,	calculate_eset = TRUE
,	calculate_pumaPCAs = TRUE
,	calculate_bcomb = TRUE
,	mmgmosComparisons = FALSE
)

Arguments

ExpressionFeatureSet

An object of class FeatureSet.

data_dir

A character string specifying where data files are stored.

load_ExpressionFeatureSet

Boolean. Load a pre-existing ExpressionFeatureSet object? Note that this has to be named "ExpressionFeatureSet.rda" and be in the data_dir directory.

calculate_eset

Boolean. Calculate ExpressionSet from ExpressionFeatureSet object? If FALSE, files named "eset\_mmgmos.rda" and "eset\_rma.rda" must be available in the data\_dir directory.

calculate_pumaPCAs

Boolean. Calculate pumaPCA from eset\_mmgmos object? If FALSE, a file named "pumaPCA\_results.rda" must be available in the data\_dir directory.

calculate_bcomb

Boolean. Calculate pumaComb from eset\_mmgmos object? If FALSE, files named "eset\_comb.rda" and "eset\_normd\_comb.rda" must be available in the data\_dir directory.

mmgmosComparisons

Boolean. If TRUE, will compare mmgmos with default settings, with mmgmos used with background correction.

Value

No return values. Various objects are saved as .rda files during the execution of this function, and various PDF files are created.

Author(s)

Richard D. Pearson

See Also

Related methods pumaDE, createDesignMatrix and createContrastMatrix

Examples

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##	Code commented out to ensure checks run quickly
#	if (require(pumadata)) data(oligo.estrogen)
#	pumaFull(oligo.estrogen)

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