caret (version 6.0-24)

Alternate Affy Gene Expression Summary Methods.: 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

# 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")