getXAM.ChipEffectFile: Gets the physical position, log-intensities and log-ratios of...

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

Gets the physical position, log-intensities and log-ratios of chip effects for two arrays

Description

Gets the physical position, log-intensities and log-ratios of chip effects for two arrays of units on a certain chromosome.

Usage

## S3 method for class 'ChipEffectFile'
getXAM(this, other, chromosome, units=NULL, ..., verbose=FALSE)

Arguments

other	The second ChipEffectFile object used as the reference.
chromosome	(The chromosome for which results should be returned.
units	(The subset of units to be matched. If NULL, all units are considered.
...	Not used.
verbose	See Verbose.

Value

Returns a Nx3 matrix where N is the number of units returned. The names of the columns are X (physical position in a given chromosome), A (log-intensities) and M (log-ratios). The names of the rows are the unit indices (as indexed by the CDF). Note: The rows are ordered according to chromosomal position.

Author(s)

Henrik Bengtsson

See Also

*getAM(). For more information see ChipEffectFile.

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