The data from the estrogen package processed using the pumaPCA algorithm

Description

This data is taken from the estrogen package. It was created to be used in the vignette for the puma pacakge. It can be produced using the following code (note this could take a long time to run):

		data(eset_estrogen_mmgmos)
		pumapca_estrogen <- pumaPCA(eset_estrogen_mmgmos)
	

Usage

data(pumapca_estrogen)

Format

An pumaPCARes object containing principal components (created using pumaPCA) of 8 HG_U95Av2 arrays, in a 2 x 2 factorial design, with 2 replicates for each combination of factors. The factors are estrogen (absent of present) and time.h (10 or 48).

See Also

eset_estrogen_mmgmos

Examples

data(pumapca_estrogen)
plot(pumapca_estrogen,legend1pos="right",legend2pos="top")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(pumadata)
Loading required package: affy
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: puma
Loading required package: oligo
Loading required package: oligoClasses
Welcome to oligoClasses version 1.34.0

Attaching package: 'oligoClasses'

The following object is masked from 'package:affy':

    list.celfiles

Loading required package: Biostrings
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: IRanges
Loading required package: XVector
================================================================================
Welcome to oligo version 1.36.1
================================================================================

Attaching package: 'oligo'

The following objects are masked from 'package:affy':

    MAplot, intensity, mm, mm<-, mmindex, pm, pm<-, pmindex,
    probeNames, rma

Loading required package: mclust
Package 'mclust' version 5.2
Type 'citation("mclust")' for citing this R package in publications.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/pumadata/pumapca_estrogen.Rd_%03d_medium.png", width=480, height=480)
> ### Name: pumapca_estrogen
> ### Title: The data from the estrogen package processed using the pumaPCA
> ###   algorithm
> ### Aliases: pumapca_estrogen
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(pumapca_estrogen)
> plot(pumapca_estrogen,legend1pos="right",legend2pos="top")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>