Function to take means of probesets.

Description

Converts an ExpressionSet or AffyBatch object with one row of expression data per probeset into an ExpressionSet or AffyBatch object with one row per probe.

Usage

psmeans(eS, ind)

Arguments

Details

Each entry of ind corresponds to one probe and tells the number of the probeset it belongs to. See tranestAffyProbeLevel and sample.ind for examples.

Value

Returns an ExpressionSet or AffyBatch object with the expression matrix rows corresponding to probesets instead of individual probes. Elements of the returned ExpressionSet or AffyBatch object are means over each probeset.

Author(s)

John Tillinghast

See Also

tranestAffyProbeLevel, sample.ind

Examples

library(LMGene)
library(Biobase)

data(sample.eS)
data(sample.ind)

# glog transform data
trs.eS <- transeS (sample.eS, 667, 65) 

# lowess normalize
ntrs.eS <- lnormeS(trs.eS) 

# take means over probesets
genesample.eS<- psmeans (ntrs.eS, sample.ind)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(LMGene)
Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: multtest
Loading required package: survival
Loading required package: affy

Attaching package: 'LMGene'

The following object is masked from 'package:base':

    norm

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/LMGene/psmeans.Rd_%03d_medium.png", width=480, height=480)
> ### Name: psmeans
> ### Title: Function to take means of probesets.
> ### Aliases: psmeans
> ### Keywords: manip
> 
> ### ** Examples
> 
> library(LMGene)
> library(Biobase)
> 
> data(sample.eS)
> data(sample.ind)
> 
> # glog transform data
> trs.eS <- transeS (sample.eS, 667, 65) 
> 
> # lowess normalize
> ntrs.eS <- lnormeS(trs.eS) 
> 
> # take means over probesets
> genesample.eS<- psmeans (ntrs.eS, sample.ind)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>