Description Usage Arguments Value Author(s) References See Also Examples
View source: R/gcrma.bg.adjust.optical.R
Adjusts for optical background by subtracting the minimum intensity per microarray (column).
1 2 | gcrma.bg.adjust.optical( abatch, minimum=1, which.probes="all", verbose = TRUE, cl)
gcrma.bg.adjust.optical.matrix( x, minimum=1, verbose = TRUE, cl)
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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 |
verbose |
Print progress messages. |
cl |
Optional paramter. A cluster object created by the |
A AffyBatch object with (optical) background adjusted intensities. A matrix with (optical) background adjusted intensities.
Johannes Rainer
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
gcrma.compute.affinities.local.pmonly
, gcrma.adjust.nomm
1 2 3 4 5 | ## 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 )
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