combine {matchprobes}R Documentation

A function to combine data from different Affymetrix genechip types into one AffyBatch.

Description

The function takes two AffyBatches and their respective probe sequence information and merges the intensities from the matching probes only into one AffyBatch.

Usage

combine(batch, probepkg, newcdf, verbose=TRUE)

Arguments

batch A list of two AffyBatches.
probepkg A character vector of length 2, containing the names of the probe sequences libraries (for example, hgu133aprobe) that go with the AffyBatches.
newcdf The name of the name CDF environment that is to be created.
verbose If TRUE, messages are printed to the console.

Details

This function is EXPERIMENTAL; no guarantee that the resulting data makes biological sense.

You may want to have a look at the code of this function and at intermediate results.

Presently the code is written for two chiptypes, but if necessary can now be easily generalized to n>=2.

Value

A list with two elements: dat, an AffyBatch, and cdf, an environment, which contains a "CDF" probe-set to probe mapping (as for ordinary genechips). cdf is obtrained by restricting the probe-set to probe of the second batch and probelib.
A vignette is being written.

Author(s)

R. Gentleman, Wolfgang Huber

Examples

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