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]) }