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