generateExprVal {affy} | R Documentation

## 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))
    }

[Package affy version 1.20.2 Index]