Method for normalizing Affymetrix Probe Level Data
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A character vector that will replace the existing one.
object is an
AffyBatch object, then
normalize(object) returns an
AffyBatch object with the
intensities normalized using the methodology specified by
getOption("BioC")$affy$normalize.method. The affy package
Other methodologies can be used by specifying them with the
method argument. For example to use the invariant set
methodology described by Li and Wong (2001) one would type:
Further arguments passed by
..., apart from
passed along to the function responsible for the methodology defined by
A character vector of nicknames for the methodologies available
is returned by
AffyBatch, or simply by
normalize.AffyBatch.methods. If the nickname of a method
is called "loess", the help page for that specific methodology can
be accessed by typing
For more on the normalization methodologies currently implemented please refer to the vignette ‘Custom Processing Methods’.
To add your own normalization procedures please refer to the customMethods vignette.
provide access to internal vectors listing the corresponding capabilities.
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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, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colSums, colnames, dirname, 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, rowMeans, rowSums, 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 connect to server' Loading required package: affydata Package LibPath Item [1,] "affydata" "/usr/local/lib/R/site-library" "Dilution" Title [1,] "AffyBatch instance Dilution"  "mas" "methods" "pmonly" "subtractmm"
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