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generateExprVal-methods

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))
}

affy

Methods for Affymetrix Oligonucleotide Arrays

v1.68.0
LGPL (>= 2.0)
Authors
Rafael A. Irizarry <rafa@ds.harvard.edu>, Laurent Gautier <lgautier@gmail.com>, Benjamin Milo Bolstad <bmb@bmbolstad.com>, and Crispin Miller <cmiller@picr.man.ac.uk> with contributions from Magnus Astrand <Magnus.Astrand@astrazeneca.com>, Leslie M. Cope <cope@mts.jhu.edu>, Robert Gentleman, Jeff Gentry, Conrad Halling <challing@agilixcorp.com>, Wolfgang Huber, James MacDonald <jmacdon@u.washington.edu>, Benjamin I. P. Rubinstein, Christopher Workman <workman@cbs.dtu.dk>, John Zhang
Initial release

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