
ExpressionSet
object.
computeExprSet(x, pmcorrect.method, summary.method, ...)
generateExprSet.methods()
upDate.generateExprSet.methods(x)
AffyBatch
holding the probe level
informations to generate the expression values, for computeExprSet,
and for upDate.generateExprSet.methods it is a character vector..ids=
can be passed. It must be a vector of
affids. The expression values will only be computed and returned for
these affyids.
The different methods available through this mechanism can be accessed
by calling the method generateExprSet.methods
with an object of
call Cel.container
as an argument.In the Affymetrix design, MM probes were included to measure the noise (or background signal). The original algorithm for background correction was to subtract the MM signal to the PM signal. The methods currently included in the package are "bg.correct.subtractmm", "bg.correct.pmonly" and "bg.correct.adjust".
To alter the available methods for generating ExprSets use upDate.generateExprSet.methods.
generateExprSet
of the class
AffyBatch
expresso
if (require(affydata)) {
data(Dilution)
ids <- c( "1000_at","1001_at")
eset <- computeExprSet(Dilution, pmcorrect.method="pmonly",
summary.method="avgdiff", ids=ids)
}
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