Background corrects probe intensities in an object of class
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An object of class
grid dimension used for mas background estimate. The array is divided into griddim equal parts. Default is 16.
arguments to pass along to the engine function.
The name of the method to apply must be double-quoted. Methods provided with the package are currently:
bg.correct.chipwide: noise correction as described in a ‘white paper’ from Affymetrix.
bg.correct.rma: the model based correction used by the RMA expression measure.
They are listed in the variable
bg.correct.methods. The user must
supply the word after "bg.correct", i.e none, subtractmm, rma, etc...
More details are available in the vignette.
R implementations similar in function to the internal implementation used by
bg.correct.rma are in
AffyBatch for which the
intensities have been background adjusted.
For some methods (RMA), only PMs are corrected and the MMs remain the
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Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, 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")'. Warning message: In read.dcf(con) : URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name' Loading required package: affydata Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'affydata'
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