Retrieve pairs of probesets used for calculating 3'/5' ratios

Description

Get the names of the qc probesets used to define the 3'/5' ratios.

Usage

 qc.get.ratios()
 qc.get.ratio(name)
 qc.add.ratio(name,probeset1,probeset2)

Arguments

Value

A list, each element with a name like gapdh3/5 and comprising of a two-element character vector of probeset IDs.

Author(s)

Crispin J Miller

References

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

See Also

setQCEnvironment qc.get.probes

Examples

  setQCEnvironment("hgu133plus2cdf")
  qc.get.ratios()
  qc.add.ratio("a.name","probeset1.id","probeset2.id")
  qc.get.ratio("a.name")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> 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.ratios.Rd_%03d_medium.png", width=480, height=480)
> ### Name:   qc.get.ratios
> ### Title: Retrieve pairs of probesets used for calculating 3'/5' ratios
> ### Aliases: ' qc.get.ratios' ' qc.get.ratio' ' qc.add.ratio'
> ### Keywords: misc
> 
> ### ** Examples
> 
>   setQCEnvironment("hgu133plus2cdf")
>   qc.get.ratios()
$`actin3/actin5`
[1] "AFFX-HSAC07/X00351_3_at" "AFFX-HSAC07/X00351_5_at"

$`actin3/actinM`
[1] "AFFX-HSAC07/X00351_3_at" "AFFX-HSAC07/X00351_M_at"

$`gapdh3/gapdh5`
[1] "AFFX-HUMGAPDH/M33197_3_at" "AFFX-HUMGAPDH/M33197_5_at"

$`gapdh3/gapdhM`
[1] "AFFX-HUMGAPDH/M33197_3_at" "AFFX-HUMGAPDH/M33197_M_at"

>   qc.add.ratio("a.name","probeset1.id","probeset2.id")
>   qc.get.ratio("a.name")
[1] "probeset1.id" "probeset2.id"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>