simpleaffy (version 2.48.0)

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

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"

Value

An object of class PairComp

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.

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)