Perform quantile normalization on the columns of a matrix or ExpressionSet
Usage
quantileNorm(x)
Arguments
x
ExpressionSet or matrix
Value
Returns x with quantile normalized columns
Author(s)
David Rossell
Examples
x <- cbind(rnorm(1000),rnorm(1000,2,4))
boxplot(x)
xnorm <- quantileNorm(x)
boxplot(xnorm)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(casper)
Loading required package: Biobase
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/casper/quantileNorm.Rd_%03d_medium.png", width=480, height=480)
> ### Name: quantileNorm
> ### Title: Apply quantile normalization
> ### Aliases: quantileNorm quantileNorm,ExpressionSet-method
> ### quantileNorm,matrix-method
> ### Keywords: manip
>
> ### ** Examples
>
> x <- cbind(rnorm(1000),rnorm(1000,2,4))
> boxplot(x)
>
> xnorm <- quantileNorm(x)
> boxplot(xnorm)
>
>
>
>
>
> dev.off()
null device
1
>