A function to transform a ProbeSet

Description

A function to transform the PMs and MMs in a ProbeSet.

Usage

## S3 method for class 'ProbeSet'
transform(`_data`, fun = I, ...)

Arguments

Details

The function fun is applied to the slots pm and mm. The function vsnh in the package vsn is a recommended argument for fun.

Value

An object of class ProbeSet.

Note

This function should make to the package affy for the version 1.4.x.

Author(s)

Laurent

Examples

library(affydata)

data(Dilution)

ppset.name <- sample(featureNames(Dilution), 1)
ppset <- probeset(Dilution, ppset.name)[[1]]
ppset.log <- transform(ppset, fun=log)

par(mfrow=c(1,2))
plot(ppset)
plot(ppset.log)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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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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> library(affypdnn)
Loading required package: affy
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")'.

registering new summary method 'pdnn'.
registering new pmcorrect method 'pdnn' and 'pdnnpredict'.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/affypdnn/transform.ProbeSet.Rd_%03d_medium.png", width=480, height=480)
> ### Name: transform.ProbeSet
> ### Title: A function to transform a ProbeSet
> ### Aliases: transform.ProbeSet
> ### Keywords: manip
> 
> ### ** Examples
> 
> library(affydata)
     Package    LibPath                            Item      
[1,] "affydata" "/home/ddbj/local/lib64/R/library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"
> 
> data(Dilution)
> 
> ppset.name <- sample(featureNames(Dilution), 1)

Warning messages:
1: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'hgu95av2cdf' 
2: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'hgu95av2cdf' 
> ppset <- probeset(Dilution, ppset.name)[[1]]
> ppset.log <- transform(ppset, fun=log)
> 
> par(mfrow=c(1,2))
> plot(ppset)
> plot(ppset.log)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>