Plot the positive controls

Description

Function for retrieving and plotting the biotin and housekeeping controls for an expression array. We know these controls should show high signal and are therefore useful for QA purposes. The housekeeping control targets a bead-type believed to be universally expressed whereas the biotin control targets the biotin used for staining.

Usage

poscontPlot(BLData, array = 1, transFun = logGreenChannelTransform, positiveControlTags = c("housekeeping", "biotin"), colList = c("red", "blue"), controlProfile = NULL, ...)

Arguments

Details

Function for plotting the observed intensites for all replicates of the specified control probes on a given array-section. The identity of the control probes can be specified by passing a ControlProfile data frame, with the first column being a vector of ArrayAddress IDs and the second column being a corresponding set of characters tags. The beads to be plotted are found by matching the positiveControlTags argument to these character tags. Users with expression data can have the ControlProfile data frame defining automatically within the function, provided the annotation of the beadLevelData object has been defined by readIllumina or setAnnotation.

Value

Plot to current graphical device

Author(s)

Mark Dunning

References

www.illumina.com/downloads/GX_QualityControl_TechNote.pdf

Examples

###Load the example beadLevelData and associated controlProfile

if(require(beadarrayExampleData)){


data(exampleBLData)

poscontPlot(exampleBLData, array=1)

poscontPlot(exampleBLData, array=2)

}

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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> library(beadarray)
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: ggplot2
Welcome to beadarray version 2.22.2
beadarray versions >= 2.0.0 are substantial updates from beadarray 1.16.0 and earlier. Please see package vignette for details
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/beadarray/poscontPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: poscontPlot
> ### Title: Plot the positive controls
> ### Aliases: poscontPlot
> ### Keywords: hplots
> 
> ### ** Examples
> 
> 
> ###Load the example beadLevelData and associated controlProfile
> 
> if(require(beadarrayExampleData)){
+ 
+ 
+ data(exampleBLData)
+ 
+ poscontPlot(exampleBLData, array=1)
+ 
+ poscontPlot(exampleBLData, array=2)
+ 
+ }
Loading required package: beadarrayExampleData
Loading required package: illuminaHumanv3.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: org.Hs.eg.db


Annotating control probes using package illuminaHumanv3.db Version:1.26.0

Annotating control probes using package illuminaHumanv3.db Version:1.26.0

> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>