averageProbes: averageProbes

In codelink: Manipulation of Codelink microarray data

Description

Takes a CodelinkSet object and computes the average (mean) and sd of duplicated probes.

Usage

	averageProbes(object, parallel = FALSE)

Arguments

object	an object of class "CodelinkSet".
parallel	whether to use a parallel version (requires package multicore).

Details

This function will compute the mean() and sd() on each duplicated probe (i.e. identical probe id as for probeNames(). CodelinkSet objects use the per-array index to enable unique identifiers needed for ExpressionSet derived objects. Although the method probeNames() provides access to Codelink probe ids, this is inconvenient when dealing with other packages that make use of featureNames() to obtain probe ids and feed them to the corresponding annotation package.

In such cases CodelinkSet objects are not compatible with methods working on ExpressionSet objects. To avoid this limitation it is possible to construct a CodelinkSet object containing unique identifiers (CodelinkSetUnique class) by averaging the intensities of all replicated probes. This is done by computing the mean(). The sd() is also computed and stored in the slot sd.

The current implementation takes a lot of time so a parallelized version of lapply() may be used through the package 'multicore'. This is controlled by the argument 'parallel' which is FALSE by default.

According to the authors it is not actually possible to use 'multicore' in a GUI environment like the R.app Cocoa application in R, because this interferes with the events loop. Therefore it is adviced to use option 'parallel=TRUE' in an R session running in a shell.

Author(s)

Diego Diez

Examples

## Not run: 
    data(codelink.example)
	foo <- averageProbes(codelink.example)

## End(Not run)

codelink documentation built on Nov. 8, 2020, 8:19 p.m.