Array-array intensity correlation plot

Description

Creates the sixth page of the QC report created by QCReport for an object of class AffyBatch The page displays array-array intensity correlation coefficients.

Usage

correlationPlot(object)

Arguments

Details

This creates the sixth page of a QCReport report. The page displays array-array intensity correlation coefficients for all pairs of arrays in an AffyBatch object. Arrays are ordered according to phenotypic data if available. This plot is useful for detecting outlier arrays.

More details are available in the vignette.

Value

TRUE

Examples

   library(affydata)
    
   data(Dilution)

  correlationPlot(Dilution)

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 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(affyQCReport)
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: affy
Loading required package: lattice
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/affyQCReport/correlationPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: correlationPlot
> ### Title: Array-array intensity correlation plot
> ### Aliases: correlationPlot QCReport-correlationPlot
> ### Keywords: hplot
> 
> ### ** Examples
> 
> 
>    library(affydata)
     Package    LibPath                            Item      
[1,] "affydata" "/home/ddbj/local/lib64/R/library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"
>     
>    data(Dilution)
> 
>   correlationPlot(Dilution)
[1] TRUE
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>