Question: Does factDesign deal with two-color data?
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gravatar for De-Jian ZHAO
10.5 years ago by
De-Jian ZHAO240
De-Jian ZHAO240 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]]
ADD COMMENTlink modified 10.5 years ago by Denise Scholtens70 • written 10.5 years ago by De-Jian ZHAO240
Answer: Does factDesign deal with two-color data?
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gravatar for rgentleman
10.5 years ago by
rgentleman5.5k
United States
rgentleman5.5k wrote:
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
ADD COMMENTlink written 10.5 years ago by rgentleman5.5k
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]] > > > > _______________________________________________ > > Bioconductor mailing list > > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- ----------------------------------------------------- Dr. Alberto Goldoni Bologna, Italy ----------------------------------------------------- [[alternative HTML version deleted]]
ADD REPLYlink written 10.5 years ago by Alberto Goldoni420
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
ADD REPLYlink written 10.5 years ago by De-Jian ZHAO240
Answer: Does factDesign deal with two-color data?
0
gravatar for Denise Scholtens
10.5 years ago by
Denise Scholtens70 wrote:
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 On Jun 11, 2009, at 4:40 AM, 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 >
ADD COMMENTlink written 10.5 years ago by Denise Scholtens70
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