AffyBatch
object into an ExpressionSet
object using the robust multi-array average (RMA) expression measure.
rma(object, subset=NULL, verbose=TRUE, destructive=TRUE, normalize=TRUE, background=TRUE, bgversion=2, ...)
AffyBatch
object.TRUE
, it writes out some messages
indicating progress. If FALSE
nothing should be printed.TRUE
, works on the PM matrix
in place as much as possible, good for large datasets.TRUE
, normalize data using
quantile normalization.TRUE
, background correct
using RMA background correction.Note that this expression measure is given to you in log base 2 scale. This differs from most of the other expression measure methods.
Please note that the default background adjustment method was changed during
the lead up to the Bioconductor 1.2 release. This means that this function and
expresso
should give results that directly agree.
Bolstad, B.M., Irizarry R. A., Astrand M., and Speed, T.P. (2003), A Comparison of Normalization Methods for High Density Oligonucleotide Array Data Based on Bias and Variance. Bioinformatics 19(2):185-193
Irizarry, RA, Hobbs, B, Collin, F, Beazer-Barclay, YD, Antonellis, KJ, Scherf, U, Speed, TP (2003) Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data. Biostatistics .Vol. 4, Number 2: 249-264
expresso
if (require(affydata)) {
data(Dilution)
eset <- rma(Dilution)
}
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