Retrieve QC probeset names for the current array type

Description

Get the names of probesets used to calculate 3'/5' ratios for the current array type. qc.get.spikes is used to set the spike probe names (i.e. bioB, bioC, etc.)

Usage

 qc.get.probes()
 qc.get.probe(name)
 qc.add.probe(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.spikes

Examples

  setQCEnvironment("hgu133plus2cdf")
  qc.get.probes()
  qc.add.probe("my.name","a.probesetid_at")
  qc.add.probe("another.name","another.probesetid_at")
  qc.get.probes()

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.probes.Rd_%03d_medium.png", width=480, height=480)
> ### Name:   qc.get.probes
> ### Title: Retrieve QC probeset names for the current array type
> ### Aliases: ' qc.get.probes' ' qc.get.probe' ' qc.add.probe'
> ### Keywords: misc
> 
> ### ** Examples
> 
>   setQCEnvironment("hgu133plus2cdf")
>   qc.get.probes()
                     actin3                      actin5 
  "AFFX-HSAC07/X00351_3_at"   "AFFX-HSAC07/X00351_5_at" 
                     actinM                      gapdh3 
  "AFFX-HSAC07/X00351_M_at" "AFFX-HUMGAPDH/M33197_3_at" 
                     gapdh5                      gapdhM 
"AFFX-HUMGAPDH/M33197_5_at" "AFFX-HUMGAPDH/M33197_M_at" 
>   qc.add.probe("my.name","a.probesetid_at")
>   qc.add.probe("another.name","another.probesetid_at")
>   qc.get.probes()
                     actin3                      actin5 
  "AFFX-HSAC07/X00351_3_at"   "AFFX-HSAC07/X00351_5_at" 
                     actinM                      gapdh3 
  "AFFX-HSAC07/X00351_M_at" "AFFX-HUMGAPDH/M33197_3_at" 
                     gapdh5                      gapdhM 
"AFFX-HUMGAPDH/M33197_5_at" "AFFX-HUMGAPDH/M33197_M_at" 
                    my.name                another.name 
          "a.probesetid_at"     "another.probesetid_at" 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>