affy (version 1.50.0)

ppsetApply: Apply a function over the ProbeSets in an AffyBatch

Description

Apply a function over the ProbeSets in an AffyBatch

Usage

ppsetApply(abatch, FUN, genenames = NULL, ...)
ppset.ttest(ppset, covariate, pmcorrect.fun = pmcorrect.pmonly, ...)

Arguments

abatch

an object inheriting from AffyBatch.

ppset

an object of class ProbeSet.

covariate

the name a covariate in the slot phenoData.

pmcorrect.fun

a function to correct PM intensities.

FUN

a function working on a ProbeSet.

genenames

a list of Affymetrix probesets ids to work with. All probe set ids used when NULL.

...

optional parameters to the function FUN.

Value

Returns a list of objects, or values, as returned by the function FUN for each ProbeSet it processes.

See Also

ProbeSet-class

Examples

ppset.ttest <- function(ppset, covariate, pmcorrect.fun = pmcorrect.pmonly, ...) {
  probes <- do.call("pmcorrect.fun", list(ppset))
  my.ttest <- function(x) {
    y <- split(x, get(covariate))
    t.test(y[[1]], y[[2]])$p.value
  }
  r <- apply(probes, 1, my.ttest)
  return(r)
}
##this takes a long time - and rowttests is a good alternative
## eg: rt = rowttests(exprs(Dilution), Dilution$liver)
## Not run: 
#   data(Dilution)
#   all.ttest <- ppsetApply(Dilution, ppset.ttest, covariate="liver")
# ## End(Not run)