Compute a summary expression value from the probes intensities
Compute a summary expression value from the probes intensities
express.summary.stat(x, pmcorrect, summary, ...) express.summary.stat.methods() # vector of names of methods upDate.express.summary.stat.methods(x)
x |
a ( |
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...) |
Returns a vector of expression values.
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)) }
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