get.fold.change.and.t.test: Compute fold change and t-test statistics between two...

In simpleaffy: Very simple high level analysis of Affymetrix data

Description

Generate fold changes (and possibly means) for a pair of experimental groups

Usage

  get.fold.change.and.t.test(x,group,members,logged = TRUE,a.order=NULL,b.order=NULL,method=c("unlogged","logged","median"));

Arguments

x	an ExpressionSet object.
group	column in pData(x).
members	labels in group.
logged	is the AffyBatch data logged?
a.order	For a pairwise comparison the ordering of the first group of replicates
b.order	For a pairwise comparison the ordering of the second group of replicates
method	What method should be used to calculate the average for the fold-change - can be either "logged","unlogged","median"

Details

Given an ExpressionSet object, generate quick stats for pairwise comparisons between a pair of experimental groups. If a.order and b.order are specified then a paired sample t-test will be conducted between the groups, with the arrays in each group sorted according to the ordering specified.

The fold-changes are computed from the average values across replicates. By default this is done using the mean of the unlogged values. The parameter, method allows the mean of the logged values or the median to be used instead. T-tests are always computed with the logged data.

Value

An object of class PairComp

Author(s)

Crispin J Miller

References

http://bioinformatics.picr.man.ac.uk/

Examples

  ## Not run: 
    pc <- get.fold.change.and.t.test(eset.rma,"group",c("A","P"))
  
## End(Not run)

simpleaffy documentation built on Nov. 8, 2020, 11:09 p.m.