generateExprSet-method {affy} | R Documentation |
Generate a set of expression values from the probe pair information. The set of expression is returned as an exprSet object.
computeExprSet(x, pmcorrect.method, summary.method, ...) generateExprSet.methods
x |
a AffyBatch holding the probe level
informations to generate the expression values. |
pmcorrect.method |
the method used to correct PM values (see section 'details'). |
summary.method |
the method used to generate the expression value (see section 'details'). |
... |
any of the options of the normalization you would like to modify |
An extra argument 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 mecanism 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 inclluded in the package are "bg.correct.subtractmm", "bg.correct.pmonly" and "bg.correct.adjust".
method generateExprSet
of the class
AffyBatch
expresso
data(affybatch.example) ids <- c( "A28102_at","AB000114_at") eset <- computeExprSet(affybatch.example, pmcorrect.method="pmonly", summary.method="avgdiff", ids=ids)