metrics: Accessing metrics information in bead-level objects

In beadarray: Quality assessment and low-level analysis for Illumina BeadArray data

Description

The metrics, p95 and snr methods conveniently access metrics information that is stored in a beadLevelData object. These data are generated by the Illumina scanning software and can be an early indicator of array quality. These include the 95th (P95) and 5th (P05) quantiles of all pixel intensities on the image. A signal-to-noise ratio (SNR) can be calculated as the ratio of these two quantities. These metrics can be viewed in real-time as the arrays themselves are being scanned. By tracking these metrics over time, one can potentially halt problematic experiments before they even reach the analysis stage. Illumina recommend that the SNR ratio should be above 10, so these arrays are acceptable. However, the P95 and P05 values will fluctuate over time and are dependant upon the scanner setup. Including SNR values for arrays other than those currently being analysed will give a better indication of whether any outlier arrays exist.

Author(s)

Mark Dunning

Examples

    if(require(beadarrayExampleData)){

        data(exampleBLData)

        metrics(exampleBLData)

        p95(exampleBLData, "Grn")

        snr(exampleBLData, "Grn")

    }

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, 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, 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: ggplot2
Welcome to beadarray version 2.24.0
Loading required package: beadarrayExampleData
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'beadarrayExampleData'

beadarray documentation built on Nov. 8, 2020, 4:51 p.m.