Alternate Affy Gene Expression Summary Methods. {caret} | R Documentation |
Generate Expression Values from Probes
Description
Generate an expression from the probes
Usage
generateExprVal.method.trimMean(probes, trim = 0.15)
Arguments
probes |
a matrix of probe intensities with rows representing
probes and columns representing
samples. Usually pm(probeset) where probeset is a
of class ProbeSet |
trim |
the fraction (0 to 0.5) of observations to be trimmed
from each end of the data before the mean is computed. |
Value
A list containing entries:
exprs |
The expression values. |
se.exprs |
The standard error estimate. |
See Also
generateExprSet-methods
Examples
## Not run:
# first, let affy/expresso know that the method exists
express.summary.stat.methods <- c(express.summary.stat.methods, "trimMean")
example not run, as it would take a while
RawData <- ReadAffy(celfile.path=FilePath)
expresso(RawData,
bgcorrect.method="rma",
normalize.method="quantiles",
normalize.param = list(type= "pmonly"),
pmcorrect.method="pmonly",
summary.method="trimMean")
step1 <- bg.correct(RawData, "rma")
step2 <- normalize.AffyBatch.quantiles(step1)
step3 <- computeExprSet(step2, "pmonly", "trimMean")
## End(Not run)
[Package
caret version 4.10
Index]