Sample PCA plot from variance-stabilized data

Description

This plot helps to check for batch effects and the like.

Usage

plotPCA(x, intgroup = "condition", ntop = 500)

Arguments

Value

a plot is produced

Author(s)

Wolfgang Huber

See Also

varianceStabilizingTransformation

Examples

cds <- makeExampleCountDataSet()
cds <- estimateSizeFactors( cds )
cds <- estimateDispersions( cds, method="blind" )
vsd <- varianceStabilizingTransformation( cds )
plotPCA( vsd )

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(DESeq)
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

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: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: lattice
    Welcome to 'DESeq'. For improved performance, usability and
    functionality, please consider migrating to 'DESeq2'.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DESeq/plotPCA.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotPCA
> ### Title: Sample PCA plot from variance-stabilized data
> ### Aliases: plotPCA
> 
> ### ** Examples
> 
> cds <- makeExampleCountDataSet()
> cds <- estimateSizeFactors( cds )
> cds <- estimateDispersions( cds, method="blind" )
> vsd <- varianceStabilizingTransformation( cds )
> plotPCA( vsd )
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>