generateExprVal-methods: Compute a summary expression value from the probes...

In Bioconductor/affy: Methods for Affymetrix Oligonucleotide Arrays

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

x	a (ProbeSet
pmcorrect	the method used to correct the PM values before summarizing to an expression value.
summary	the method used to generate the expression value.
...	other parameters the method might need... (see the corresponding methods below...)

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))
}

Bioconductor/affy documentation built on July 21, 2023, 5:23 p.m.