ppsetApply: Apply a function over the ProbeSets in an AffyBatch
In affy: Methods for Affymetrix Oligonucleotide Arrays

Description Usage Arguments Value Author(s) See Also Examples

Apply a function over the ProbeSets in an AffyBatch

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ppsetApply(abatch, FUN, genenames = NULL, ...)

ppset.ttest(ppset, covariate, pmcorrect.fun = pmcorrect.pmonly, ...)

`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`.

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

Laurent Gautier <laurent@cbs.dtu.dk>

ProbeSet-class

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)