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