rma: Robust Multi-Array Average expression measure

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/rma.R


This function converts an 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, ...)



an AffyBatch object.


a character vector with the the names of the probesets to be used in expression calculation.


logical value. If TRUE, it writes out some messages indicating progress. If FALSE nothing should be printed.


logical value. If TRUE, works on the PM matrix in place as much as possible, good for large datasets.


logical value. If TRUE, normalize data using quantile normalization.


logical value. If TRUE, background correct using RMA background correction.


integer value indicating which RMA background to use 1: use background similar to pure R rma background given in affy version 1.0 - 1.0.2 2: use background similar to pure R rma background given in affy version 1.1 and above


further arguments to be passed (not currently implemented - stub for future use).


This function computes the RMA (Robust Multichip Average) expression measure described in Irizarry et al Biostatistics (2003).

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.


An ExpressionSet


Ben Bolstad bmb@bmbolstad.com


Rafael. A. Irizarry, Benjamin M. Bolstad, Francois Collin, Leslie M. Cope, Bridget Hobbs and Terence P. Speed (2003), Summaries of Affymetrix GeneChip probe level data Nucleic Acids Research 31(4):e15

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

See Also



if (require(affydata)) {
  eset <- rma(Dilution)

Example output

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package:BiocGenericsThe following objects are masked frompackage:parallel:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked frompackage:stats:

    IQR, mad, sd, var, xtabs

The following objects are masked frompackage:base:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: affydata
     Package    LibPath                   Item      
[1,] "affydata" "/usr/lib/R/site-library" "Dilution"
[1,] "AffyBatch instance Dilution"

Background correcting
Calculating Expression
Warning messages:
1: replacing previous importAnnotationDbi::tailbyutils::tailwhen loadinghgu95av2cdf2: replacing previous importAnnotationDbi::headbyutils::headwhen loadinghgu95av2cdf

affy documentation built on Nov. 8, 2020, 8:18 p.m.