Get or set the alpha values for the current QC environment

Description

Alpha1 and Alpha2 are used to define the P/M/A thresholds for detection calling algorithm see - detection.p.val. These are array dependent, these functions set or get their values. Tau is a constant parameter within the calculation and is not array specific.

Usage

 qc.get.alpha1()
 qc.set.alpha1(value)
 qc.get.alpha2()
 qc.set.alpha2(value)
 qc.get.tau()

Arguments

Value

qc.set.alpha1 and qc.set.alpha2 return nothing. qc.get.alpha1 and qc.get.alpha2 return a double.

Author(s)

Crispin J Miller

References

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

See Also

detection.p.val

Examples

  setQCEnvironment("hgu133plus2cdf")
  qc.get.alpha1()
  qc.get.alpha2()
  qc.set.alpha1(0.05)
  qc.get.alpha1()
  qc.set.alpha2(0.05)
  qc.get.alpha2()

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.alpha1.Rd_%03d_medium.png", width=480, height=480)
> ### Name:   qc.get.alpha1
> ### Title: Get or set the alpha values for the current QC environment
> ### Aliases: ' qc.get.alpha1' ' qc.set.alpha1' ' qc.get.alpha2' '
> ###   qc.set.alpha2' ' qc.get.tau '
> ### Keywords: misc
> 
> ### ** Examples
> 
>   setQCEnvironment("hgu133plus2cdf")
>   qc.get.alpha1()
[1] 0.05
>   qc.get.alpha2()
[1] 0.065
>   qc.set.alpha1(0.05)
>   qc.get.alpha1()
[1] 0.05
>   qc.set.alpha2(0.05)
>   qc.get.alpha2()
[1] 0.05
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>