Compute a summary expression value from the probes intensities

Description

Compute a summary expression value from the probes intensities

Usage

express.summary.stat(x, pmcorrect, summary, ...)
express.summary.stat.methods() # vector of names of methods
upDate.express.summary.stat.methods(x)

Arguments

Value

Returns a vector of expression values.

Examples

if (require(affydata)) {
  data(Dilution)

  p <- probeset(Dilution, "1001_at")[[1]]

  par(mfcol=c(5,2))
  mymethods <- express.summary.stat.methods()
  nmet <- length(mymethods)
  nc <- ncol(pm(p))

  layout(matrix(c(1:nc, rep(nc+1, nc)), nc, 2), width = c(1, 1))

  barplot(p)

  results <- matrix(0, nc, nmet)
  rownames(results) <- paste("sample", 1:nc)
  colnames(results) <- mymethods

  for (i in 1:nmet) {
    ev <- express.summary.stat(p, summary=mymethods[i], pmcorrect="pmonly")
    if (mymethods[[i]] != "medianpolish")
      results[, i] <- 2^(ev$exprs)
    else
      results[, i] <- ev$exprs
  }

  dotchart(results, labels=paste("sample", 1:nc))
}

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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> library(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")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/affy/generateExprVal-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: generateExprVal
> ### Title: Compute a summary expression value from the probes intensities
> ### Aliases: express.summary.stat express.summary.stat-methods
> ###   express.summary.stat.methods upDate.express.summary.stat.methods
> ### Keywords: manip
> 
> ### ** Examples
> 
> if (require(affydata)) {
+   data(Dilution)
+ 
+   p <- probeset(Dilution, "1001_at")[[1]]
+ 
+   par(mfcol=c(5,2))
+   mymethods <- express.summary.stat.methods()
+   nmet <- length(mymethods)
+   nc <- ncol(pm(p))
+ 
+   layout(matrix(c(1:nc, rep(nc+1, nc)), nc, 2), width = c(1, 1))
+ 
+   barplot(p)
+ 
+   results <- matrix(0, nc, nmet)
+   rownames(results) <- paste("sample", 1:nc)
+   colnames(results) <- mymethods
+ 
+   for (i in 1:nmet) {
+     ev <- express.summary.stat(p, summary=mymethods[i], pmcorrect="pmonly")
+     if (mymethods[[i]] != "medianpolish")
+       results[, i] <- 2^(ev$exprs)
+     else
+       results[, i] <- ev$exprs
+   }
+ 
+   dotchart(results, labels=paste("sample", 1:nc))
+ }
Loading required package: affydata
     Package    LibPath                            Item      
[1,] "affydata" "/home/ddbj/local/lib64/R/library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"

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' 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>