getRelSignStrength: functions to perform SPLICE
In splicegear: splicegear

Description Usage Arguments Details Value Author(s) References Examples

Implementations of the SPLICE algorithm

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getRelSignStrength(x, tissue = as.factor(1:ncol(x)), fun = mean, nipt = 30, nitt = 30, ...)

getFinalRatio(x, tissue=as.factor(1:ncol(x)), fun=mean, ...)

`x`	a matrix. One probe per line, one column per sample. Typically this would be the slot `exprs` of an instance of class `ExprSet`.
`tissue`	a covariate (factor) about the samples.
`fun`	a function to obtain a summary value (`mean` by default)
`nipt`	see reference.
`nitt`	see reference.
`...`	optional parameters for the function `fun`

getFinalRatio will call getRelSignStrength. The values are log-transformed. It is probably a good idea to avoid feeding function with values that are already on log scale.

A matrix of the same dimension than the input x, holding 'RSS' (Relative Signal Strength) or 'final ratios' respectively, as described in the reference. Two attributes nip and nit are attached the returned matrix.

laurent@cbs.dtu.dk

Genome Research (2001), Hu et. al., vol. 11, p.1244

data(spliceset)

## The intensity values in the example are log-transformed.
## Undo by taking the exponential
exprs(spliceset) <- exp(exprs(spliceset))

## Re-order the rows of different slots to have the probes sorted by
## position
spliceset <- sort.SpliceExprSet(spliceset)
## extract the expression matrix
expr.m <- exprs(spliceset)
fr <- getFinalRatio(expr.m, tissue=pData(spliceset@eset)[[1]])