expresso: 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 adjustment 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, an 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).

Value

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

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.

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.

Examples

Run this code

if (require(affydata)) {
  data(Dilution)

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

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