Retrieve QC spike probeset names for the current array type

Description

Get the names of spike probesets for bioB, bioC, etc. ratios for the current array type. qc.get.probes is used to define the 3'/5' ratio probesets

Usage

 qc.get.spikes()
 qc.get.spike(name)
 qc.add.spike(name,probeset)

Arguments

Value

A character array of probeset IDs, or the requested probeset ID, as appropriate.

Author(s)

Crispin J Miller

References

http://bioinformatics.picr.man.ac.uk/

See Also

setQCEnvironment qc.get.probes

Examples

  qc.get.spikes()
  qc.add.spike("my.name","a.probesetid_at")
  qc.add.spike("another.name","another.probesetid_at")
  qc.get.spikes()

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 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> library(simpleaffy)
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: affy
Loading required package: genefilter
Loading required package: gcrma
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/simpleaffy/qc.get.spikes.Rd_%03d_medium.png", width=480, height=480)
> ### Name:   qc.get.spikes
> ### Title: Retrieve QC spike probeset names for the current array type
> ### Aliases: ' qc.get.spikes' ' qc.get.spike' ' qc.add.spike'
> ### Keywords: misc
> 
> ### ** Examples
> 
>   qc.get.spikes()
Error in .qc.test() : QC environment is empty.
 See 'setQCEnvironment' for more details.
Calls: qc.get.spikes -> .qc.test
Execution halted