Hi Dejian,

for this array data i have used RankProd package that is based on the rank
product method. The usage is different from affy chip and it depends on the
experimental design. It is designed for two colour arrays too.
See the vignette.

I guess with this package you can perform the analysis.

Hope this help.
Best regards.

2009/6/11 Robert Gentleman <rgentlem@fhcrc.org>

> Hi Dejian,
>  Yes, it really just requires that you have an ExpressionSet, but please
> let us
> know (on list) if any issues arise.
>
>  best wishes
>    Robert
>
>
> Dejian Zhao wrote:
> > 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*_
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
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> > Bioconductor@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
>
> --
> Robert Gentleman, PhD
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> PO Box 19024
> Seattle, Washington 98109-1024
> 206-667-7700
> rgentlem@fhcrc.org
>
> _______________________________________________
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>



-- 
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Dr. Alberto Goldoni
Bologna, Italy
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