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Question: Agilent 2-color Microarray data analysis tutorial
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gravatar for Chuming Chen
8.4 years ago by
Chuming Chen140
Chuming Chen140 wrote:
Dear All, Can anybody point a tutorial on Agilent 2-color Microarray data analysis including pre-processing, statistical analyses, Gene set enrichment analysis, Clustering and visualization etc.? Thanks, Chuming
ADD COMMENTlink modified 8.4 years ago by Martin Morgan ♦♦ 21k • written 8.4 years ago by Chuming Chen140
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gravatar for Martin Morgan
8.4 years ago by
Martin Morgan ♦♦ 21k
United States
Martin Morgan ♦♦ 21k wrote:
Hi Chuming -- Chuming Chen wrote: > Dear All, > > Can anybody point a tutorial on Agilent 2-color Microarray data analysis > including pre-processing, statistical analyses, Gene set enrichment > analysis, Clustering and visualization etc.? The limma vignette is a very useful general purpose starting point, http://bioconductor.org/packages/2.5/bioc/html/limma.html as are the workshop resources related to microarray analysis http://bioconductor.org/workshops/ and common workflows http://bioconductor.org/docs/workflows/index.html Martin > > Thanks, > > Chuming > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
ADD COMMENTlink written 8.4 years ago by Martin Morgan ♦♦ 21k
Martin Morgan wrote: > Hi Chuming -- > > Chuming Chen wrote: >> Dear All, >> >> Can anybody point a tutorial on Agilent 2-color Microarray data analysis >> including pre-processing, statistical analyses, Gene set enrichment >> analysis, Clustering and visualization etc.? > > The limma vignette is a very useful general purpose starting point, > > http://bioconductor.org/packages/2.5/bioc/html/limma.html > > as are the workshop resources related to microarray analysis > > http://bioconductor.org/workshops/ > > and common workflows > > http://bioconductor.org/docs/workflows/index.html also the Bioconductor case studies book provides a very useful extended tutorial http://bioconductor.org/pub/biocases/ > > Martin > >> Thanks, >> >> Chuming >> >> _______________________________________________ >> 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 > > -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
ADD REPLYlink written 8.4 years ago by Martin Morgan ♦♦ 21k
Dear Martin, thanks for the useful links, especially the Bioconductor case studies book. I am also interested in the Agilent 2-color data analysis. In the Bioconductor case studies book source code, the Chapter 4 Two Color Arrays is about the analysis of Agilent 2 color data processed with genepix image analysis program. I just have a question about filtering of such data. Normally filtering is done before finding differentially expressed genes (in this case with limma) and after normalization. Filtering out control probes is straightforward. What about other filtering criteria, such as IQR? How can filtering be applied to 2-color data in the form of RGlist or MAlist? Thanks, Yong Martin Morgan wrote: > Martin Morgan wrote: >> Hi Chuming -- >> >> Chuming Chen wrote: >>> Dear All, >>> >>> Can anybody point a tutorial on Agilent 2-color Microarray data analysis >>> including pre-processing, statistical analyses, Gene set enrichment >>> analysis, Clustering and visualization etc.? >> The limma vignette is a very useful general purpose starting point, >> >> http://bioconductor.org/packages/2.5/bioc/html/limma.html >> >> as are the workshop resources related to microarray analysis >> >> http://bioconductor.org/workshops/ >> >> and common workflows >> >> http://bioconductor.org/docs/workflows/index.html > > also the Bioconductor case studies book provides a very useful extended > tutorial > > http://bioconductor.org/pub/biocases/ > >> Martin >> >>> Thanks, >>> >>> Chuming >>> >>> _______________________________________________ >>> 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 REPLYlink written 8.4 years ago by Yong Li190
Yong Li wrote: > Dear Martin, > > thanks for the useful links, especially the Bioconductor case studies > book. I am also interested in the Agilent 2-color data analysis. > > In the Bioconductor case studies book source code, the Chapter 4 Two > Color Arrays is about the analysis of Agilent 2 color data processed > with genepix image analysis program. I just have a question about > filtering of such data. Normally filtering is done before finding > differentially expressed genes (in this case with limma) and after > normalization. Filtering out control probes is straightforward. What > about other filtering criteria, such as IQR? How can filtering be > applied to 2-color data in the form of RGlist or MAlist? after normalization one has an MAlist. These can be subset, so for instance one could use Biobase::rowQ on maList$M to calculate interquartile range n = nrow(maList) iqr = with(maList, rowQ(M, ceiling(.75*n)) - rowQ(M, floor(.25*n))) filtered = maList[iqr > .5,] (untested) Martin > > Thanks, > Yong > > Martin Morgan wrote: >> Martin Morgan wrote: >>> Hi Chuming -- >>> >>> Chuming Chen wrote: >>>> Dear All, >>>> >>>> Can anybody point a tutorial on Agilent 2-color Microarray data >>>> analysis >>>> including pre-processing, statistical analyses, Gene set enrichment >>>> analysis, Clustering and visualization etc.? >>> The limma vignette is a very useful general purpose starting point, >>> >>> http://bioconductor.org/packages/2.5/bioc/html/limma.html >>> >>> as are the workshop resources related to microarray analysis >>> >>> http://bioconductor.org/workshops/ >>> >>> and common workflows >>> >>> http://bioconductor.org/docs/workflows/index.html >> >> also the Bioconductor case studies book provides a very useful extended >> tutorial >> >> http://bioconductor.org/pub/biocases/ >> >>> Martin >>> >>>> Thanks, >>>> >>>> Chuming >>>> >>>> _______________________________________________ >>>> 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 >>> >> > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
ADD REPLYlink written 8.4 years ago by Martin Morgan ♦♦ 21k
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