compareLimmapumaDE: Compare pumaDE with a default Limma model

In puma: Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)

Description

This function compares the identification of differentially expressed (DE) genes using the pumaDE function and the limma package.

Usage

compareLimmapumaDE(
	eset_mmgmos
,	eset_comb = NULL
,	eset_other = eset_mmgmos
,	limmaRes = calculateLimma(eset_other)
,	pumaDERes = pumaDE(eset_comb)
,	contrastMatrix = createContrastMatrix(eset_mmgmos)
,	numberToCompareForContrasts = 3
,	numberToCompareForVenn = 100
,	plotContrasts = TRUE
,	contrastsFilename = NULL
,	plotOther = FALSE
,	otherFilename = "other"
,	plotBcombContrasts = FALSE
,	bcombContrastsFilename = "bcomb_contrasts"
,	plotVenn = FALSE
,	vennFilename = "venn.pdf"
,	showTopMatches = FALSE
,	returnResults = FALSE
)

Arguments

eset_mmgmos	An object of class ExpressionSet, that includes both expression levels as well as standard errors of the expression levels. This will often have been created using mmgmos, but might also have been created by mgmos, or any other method capable of providing standard errors.
eset_comb	An object of class ExpressionSet, includes both expression levels as well as standard errors of the expression levels for each unique condition in an experiment (i.e. created from combining the information from each replicate). This will usually have been created using pumaComb.
eset_other	An object of class ExpressionSet, that includes expression levels , and may optionally also include standard errors of the expression levels. This is used for comparison with eset_mmgmos, and might have been created by any summarisation method, e.g. rma.
limmaRes	A list with two elements, usually created using the function calculateLimma. The first element is a matrix of p-values. Each column represent one contrast. Within each column the p-values are ordered. The second element is a matrix of row numbers, which can be used to map p-values back to probe sets. If not supplied this will be automatically created from eset_other.
pumaDERes	A list with two elements, usually created using the function pumaDE. The first element is a matrix of PPLR values. Each column represent one contrast. Within each column the PPLR values are ordered. The second element is a matrix of row numbers, which can be used to map PPLR values back to probe sets. If not supplied this will be automatically created from eset_comb.
contrastMatrix	A contrast matrix. If not supplied this will be created from eset_mmgmos
numberToCompareForContrasts	An integer specifying the number of most differentially expressed probe sets (genes) that will be used in comparison charts.
numberToCompareForVenn	An integer specifying the number of most differentially expressed probe sets (genes) that will be used for comparison in the Venn diagram.
plotContrasts	A boolean specifying whether or not to plot the most differentially expressed probe sets (genes) for each contrast for the eset_mmgmos ExpressionSet.
contrastsFilename	A character string specifying a file name stem for the PDF files which will be created to hold the contrast plots for the eset_mmgmos ExpressionSet. The actually filenames will have the name of the contrast appended to this stem.
plotOther	A boolean specifying whether or not to plot the most differentially expressed probe sets (genes) for each contrast for the eset_other ExpressionSet.
otherFilename	A character string specifying a file name stem for the PDF files which will be created to hold the contrast plots for the eset_other ExpressionSet. The actually filenames will have the name of the contrast appended to this stem.
plotBcombContrasts	A boolean specifying whether or not to plot the most differentially expressed probe sets (genes) for each contrast for the eset_comb ExpressionSet.
bcombContrastsFilename	A character string specifying a file name stem for the PDF files which will be created to hold the contrast plots for the eset_comb ExpressionSet. The actually filenames will have the name of the contrast appended to this stem.
plotVenn	A boolean specifying whether or not to plot a Venn diagram showing the overlap in the most differentially expressed probe sets (genes) as identified from the two different methods being compared.
vennFilename	A character string specifying the filename for the PDF file which will hold the Venn diagram showing the overlap in the most differentially expressed probe sets (genes) as identified from the two different methods being compared.
showTopMatches	A boolean specifying whether or not to show the probe sets which are deemed most likely to be differentially expressed.
returnResults	A boolean specifying whether or not to return a list containing results generated.

Value

The main outputs from this function are a number of PDF files.

The function only returns results if returnResults=TRUE

Author(s)

Richard D. Pearson

See Also

Related methods pumaDE and calculateLimma

puma documentation built on Nov. 8, 2020, 11:08 p.m.