gcrma.bg.adjust.optical: Optical background correction

In jotsetung/generalgcrma: GCRMA background adjustment for Affymetrix Tiling, Exon and Gene ST microarrays.

Description

Adjusts for optical background by subtracting the minimum intensity per microarray (column).

Usage

gcrma.bg.adjust.optical( abatch, minimum=1, which.probes="all", verbose = TRUE, cl)
gcrma.bg.adjust.optical.matrix( x, minimum=1, verbose = TRUE, cl)

Arguments

abatch	AffyBatch object.
x	A numerical matrix with intensities.
minimum	Minimal intensity value that is added to each bg adjusted intensity (defaults to +1 and thus avoids adjusted values between 0 and 1).
which.probes	Which probes should be bg adjusted. Allowed values are all (use all probes/intensities on the array), both (all probes on the array that are either pm or mm probes), pm (only the pm probes), mm (only the mm probes).
verbose	Print progress messages.
cl	Optional paramter. A cluster object created by the makeCluster function from the snow package. If submitted a parallelized version of this function is used.

Value

A AffyBatch object with (optical) background adjusted intensities. A matrix with (optical) background adjusted intensities.

Author(s)

Johannes Rainer

References

Rainer J, Lelong J, Bindreither D, Mantinger C, Ploner C, Geley S, Kofler R. (2012) Research resource: transcriptional response to glucocorticoids in childhood acute lymphoblastic leukemia. Mol Endocrinol. 2012 Jan;26(1):178-93.

http://bioinfo.i-med.ac.at

See Also

gcrma.compute.affinities.local.pmonly, gcrma.adjust.nomm

Examples

## loading some data
data( "test.data" )

## performing a simple optical baclkground adjustment per array (adding +1 to avoid values between 0 and 1)
test.data <- gcrma.bg.adjust.optical.matrix( test.data )

jotsetung/generalgcrma documentation built on May 19, 2019, 9:41 p.m.