Many thanks for your responses. The package can deal with two-color data according to Robert. I get the answer. Thanks to Denise and Alberto for suggestions. Alberto Goldoni wrote: > 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 at="" 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]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at 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 at fhcrc.org >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> Hi Dejian, > > Currently, factDesign is not directly set up to deal with two-color > data, although the functions could be adapted easily enough. I might > recommend the limma package. The user's manual contains several > examples of two-color data analysis. > > Hope that helps - > Denise