| rma.para {RefPlus} | R Documentation |
Obtain reference quantiles and reference probe effects based on reference set Train, and calculate the gene expression
rma.para(Train, bg = TRUE, exp = FALSE)
Train |
An AffyBatch object of the reference set microarrays. |
bg |
A logical flag. If True(by default), background correct
Train using default bg.correct.rma. |
exp |
A logical flag. If True, calculate the RMA measurements of
Train. If False, return 0. |
Reference.Quantiles |
Reference quantiles derived from Train. |
probe.effects |
Estimated probe effects derived from Train. |
expression |
RMA measurements of Train. |
The RMA procedure requires a lot of computer memory.
Kai-Ming Chang(kaiming@gmail.com)
Chang,K.M., Harbron,C., South,M.C. (2006) An Exploration of Extensions to the RMA Algorithm. Available with the RefPlus package.
if (require(affydata)) {
## Use Dilution in affydata package
data(Dilution)
## Background correct, estimate the probe effects, and calculate the
## RMA intensities using rma.para function.
Ex<-rma.para(Dilution, bg=TRUE,exp=TRUE)
## Calculate the rma intensities using rma function.
Ex0<-exprs(rma(Dilution))
plot(Ex$express[,1],Ex0[,1])
}