ppsetApply: Apply a function over the ProbeSets in an AffyBatch

In Bioconductor/affy: Methods for Affymetrix Oligonucleotide Arrays

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.

Author(s)

Laurent Gautier <[e-mail]>

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)

Bioconductor/affy documentation built on July 21, 2023, 5:23 p.m.