computeAffinities.AffymetrixCdfFile: Calculates probe affinities from sequence

In HenrikBengtsson/aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

Calculates probe affinities from sequence

Description

Calculates probe affinities from sequence.

Adapted from compute.affinities in the gcrma package. Attempts to find the tab-separated probe sequence file associated with a particular CDF, and matches sequence to probe index in order to assign an affinity to each probe.

Usage

## S3 method for class 'AffymetrixCdfFile'
computeAffinities(this, safe=TRUE, force=FALSE, verbose=FALSE, ...)

Arguments

safe	A logical argument passed to getProbeSequenceData().
force	If FALSE, cached results is returned, if available.
verbose	See Verbose.
...	Not used.

Value

Returns a numeric vector of (log2) probe affinities, of length equal to the total number of features on the array.

Author(s)

Ken Simpson, Henrik Bengtsson, Mark Robinson

HenrikBengtsson/aroma.affymetrix documentation built on Feb. 20, 2024, 9:07 p.m.