expresso {affy}R Documentation

From raw probe intensities to expression values

Description

Goes from raw probe intensities to expression values

Usage

expresso(
        afbatch,
    # background correction
        bg.correct = TRUE,
        bgcorrect.method = NULL,
        bgcorrect.param = list(),
    # normalize
        normalize = TRUE,
        normalize.method = NULL,
        normalize.param = list(),
    # pm correction
        pmcorrect.method = NULL,
        pmcorrect.param = list(),
    # expression values
        summary.method = NULL,
        summary.param = list(),
        summary.subset = NULL,
    # misc.
        verbose = TRUE,
        widget = FALSE)

Arguments

afbatch An AffyBatch object
bg.correct a boolean to express whether background correction is wanted or not.
bgcorrect.method the name of the background adjustment method
bgcorrect.param a list of parameters for bgcorrect.method (if needed/wanted)
normalize normalization step wished or not.
normalize.method the normalization method to use
normalize.param a list of parameters to be passed to the normalization method (if wanted).
pmcorrect.method the name of the PM adjustement method
pmcorrect.param a list of parameters for pmcorrect.method (if needed/wanted)
summary.method the method used for the computation of expression values
summary.param a list of parameters to be passed to the summary.method (if wanted).
summary.subset a list of 'affyids'. If NULL, a expression summary value is computed for everything on the chip.
verbose logical value. If TRUE it writes out some messages.
widget a boolean to specify the use of widgets (the package tkWidget is required).

Details

Some arguments can be left to NULL if the widget=TRUE. In this case, a widget pops up and let the user choose with the mouse. The arguments are: AffyBatch, bgcorrect.method, normalize.method, pmcorrect.method and summary.method.

For the mas 5.0 and 4.0 methods ones need to normalize after obtaining expression. The function affy.scalevalue.exprSet does this.

To see what background methods are available you can look at the object bgcorrect.methods.

For the Li and Wong summary method notice you will not get the same results as you would get with dChip. dChip is not open source so it is not easy to reproduce. Notice also that this iterative algorithm will not always converge. If you run the algorithm on thousands of probes expect some non-convergence warnings. These are more likely when few arrays are used. We recommend using this method only if you have 10 or more arrays. Please refer to the fit.li.wong help page for more details.

Value

An object of class exprsSet, with an attribute pps.warnings as returned by the method computeExprSet.

See Also

AffyBatch

Examples

data(affybatch.example)

eset <- expresso(affybatch.example, bgcorrect.method="rma",
                 normalize.method="constant",pmcorrect.method="pmonly",
                 summary.method="avgdiff")

##to see options available for bg correction type:
bgcorrect.methods

[Package affy version 1.8.1 Index]