Hi,
I learned about factDesign package from a scientific  article which 
deals with affy data. 
The command library(help=factDesign) invokes some information about this 
package.
It shows that this package "Suggests:      affy".
Therefore I wonder whether the factDesign package can deal with 
two-color data.
Thanks

Dejian


Package:       factDesign
Title:         Factorial designed microarray experiment analysis
Version:       1.20.0
Author:        Denise Scholtens
Description:   This package provides a set of tools for analyzing data 
from a factorial designed microarray experiment,
               or any microarray experiment for which a linear model is 
appropriate. The functions can be used to
               evaluate tests of contrast of biological interest and 
perform single outlier detection.
Imports:       genefilter, stats
_*Suggests:      affy*_

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