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Agi4x44PreProcess
NAMESPACE:version 1.3.3
in BGandNorm, we pass the matrix MMM=RGlist$G - RGlist$Gb to the backgroundCorrect(...,normexp) function, so that only the 'green' color is computed. Internally, the backgroundCorrect(...,normexp) corrects the green and red channels if we pass an RGList. By default, the function fit a normal+exponential convolution model to a vector of background corrected intensities (RGList$G - RGList$Gb), that's why we define MMM=RGlist$G - RGlist$Gb. We specify the background signal used by backgroundCorrect() in the BGandNorm()function using the argument background

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Agi4x44PreProcess
fixed the parser warnings and made the man page more readable

[/Agi4x44PreProcess] permanent link

Agi4x44PreProcess
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.

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Agi4x44PreProcess
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.

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Agi4x44PreProcess
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.

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Agi4x44PreProcess
ddNORM$R, $Gb and $Rb have been set to ddNORM$G to avoid dimensionality problems in other functions. In ddNORM, the only field that is useful is the $G. here is where the normalized signal is stored.

changed nARR=dim(RGlist)[2] for nARR=dim(RGlist$G)[2]
Correction in BGandNorm.R, options for BG and NORM. Outpuut is RGlist$G in log2 scale. The rest of the fields, RGlist$R, $Gb and $Rb are set to NULL

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Agi4x44PreProcess
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.

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