Combining replicates for each condition with the true gene expression

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Description

This function calculates the combined (from replicates) signal for each condition using Bayesian models, which are added a hidden variable to represent the true expression for each gene on each chips. The inputs are gene expression levels and the probe-level standard deviations associated with expression measurements for each gene on each chip. The outputs include gene expression levels and standard deviation for each condition.

Usage

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pumaCombImproved(
	eset
,	design.matrix=NULL
,	numOfChunks=1000
,       maxOfIterations=200
,	save_r=FALSE
,	cl=NULL
,	parallelCompute=FALSE
)

Arguments

eset

An object of class ExpressionSet.

design.matrix

A design matrix.

numOfChunks

An integer defining how many chunks the data is divided into before processing. There is generally no need to change the default value.

maxOfIterations

The maximum number of iterations controls the convergence.

save_r

Will save an internal variable r to a file. Used for debugging purposes.

cl

A "cluster" object. See makeCluster function from snow package for more details (if available).

parallelCompute

Boolean identifying whether processing in parallel should occur.

Details

It is generally recommended that data is normalised prior to using this function. Note that the default behaviour of mmgmos is to normalise data so this shouldn't generally be an issue. See the function pumaNormalize for more details on normalisation.

The maxOfIterations is used to control the maximum number of the iterations in the EM algorithm. You can change the number of maxOfIterations, but the best value of the maxOfIterations is from 200 to 1000, and should be set 200 at least. The default value is 200.

Value

The result is an ExpressionSet object.

Author(s)

Li Zhang, Xuejun Liu

References

Gelman,A., Carlin,J.B., Stern,H.S., Rubin,D.B., Bayesian data analysis. London: Chapman & Hall; 1995.

Zhang,L. and Liu,X. (2009) An improved probabilistic model for finding differential gene expression, technical report available request. the 2nd BMEI 17-19 oct. 2009. Tianjin. China.

Liu,X., Milo,M., Lawrence,N.D. and Rattray,M. (2006) Probe-level variances improve accuracy in detecting differential gene expression, Bioinformatics, 22(17):2107-13.

See Also

Related methods pumaNormalize, hcomb, mmgmos and pumaDE

Examples

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	#	Next 4 lines commented out to save time in package checks, and saved version used
    # if (require(affydata)) {
	#	data(Dilution)
	#	eset_mmgmos <- mmgmos(Dilution)
	# }
	data(eset_mmgmos)

	#	Next line shows that eset_mmgmos has 4 arrays, each of which is a different
	#   condition (the experimental design is a 2x2 factorial, with both liver and
	#	scanner factors)
	pData(eset_mmgmos)
	
	#	Next line shows expression levels of first 3 probe sets
	exprs(eset_mmgmos)[1:3,]

	#	Next line used so eset_mmgmos only has information about the liver factor
	#	The scanner factor will thus be ignored, and the two arrays of each level
	#	of the liver factor will be treated as replicates
	pData(eset_mmgmos) <- pData(eset_mmgmos)[,1,drop=FALSE]

	#	To save time we'll just use 100 probe sets for the example
	eset_mmgmos_100 <- eset_mmgmos[1:100,]
	eset_combimproved <- pumaCombImproved(eset_mmgmos_100)
	
	#	We can see that the resulting ExpressionSet object has just two conditions
	#	and 1 expression level for each condition
	pData(eset_combimproved)
	exprs(eset_combimproved)[1:3,]

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