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))

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