Generate a set of expression values from the probe pair
information. The set of expression is returned as an
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the method used to correct PM values (see section 'details').
the method used to generate the expression value (see section 'details').
any of the options of the normalization you would like to modify.
An extra argument
ids= can be passed. It must be a vector of
affids. The expression values will only be computed and returned for
The different methods available through this mechanism can be accessed
by calling the method
generateExprSet.methods with an object of
Cel.container as an argument.
In the Affymetrix design, MM probes were included to measure the noise (or background signal). The original algorithm for background correction was to subtract the MM signal to the PM signal. The methods currently included in the package are "bg.correct.subtractmm", "bg.correct.pmonly" and "bg.correct.adjust".
To alter the available methods for generating ExprSets use upDate.generateExprSet.methods.
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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’: 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" Title [1,] "AffyBatch instance Dilution" 2 ids to be processed | | |####################| Warning messages: 1: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘hgu95av2cdf’ 2: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘hgu95av2cdf’
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