plotPCA: Sample PCA plot from variance-stabilized data

In DESeq: Differential gene expression analysis based on the negative binomial distribution

Description

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

Usage

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

Arguments

x	an ExpressionSet, as obtained from varianceStabilizingTransformation
intgroup
ntop	how many of the most variable genes should be used in calculating the PCA

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 )

Example output

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, cbind, colMeans, colSums, 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, 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")'.

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'.

DESeq documentation built on April 28, 2020, 6:37 p.m.