generateExprVal {affy}R Documentation

Compute a summary expression value from the probes intensities

Description

Compute a summary expression value from the probes intensities

Usage

generateExprVal.methods # vector of names of methods

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

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

data(affybatch.example)

p <- probeset(affybatch.example, "A28102_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))


[Package affy version 1.8.1 Index]