hi all, I have used GOstats and topGO to get the GO anotations of my Gene list. Now I hear about GSEABase can do more things about pathway analysis. I installed the GSEABase packages and study it. But I think I can't get the pathway analysis tools in GSEABase. And what is the result of GSEA pathway analysis. Anyone can help me. Best, Chunjiang [[alternative HTML version deleted]]

chunjiang he wrote: > hi all, > I have used GOstats and topGO to get the GO anotations of my Gene list. Now > I hear about GSEABase can do more things about pathway analysis. I installed > the GSEABase packages and study it. But I think I can't get the pathway GSEABase provides classes for organizing gene sets, and for accessing gene sets available in other locations (such as those at the Broad). It does not provide gene set analysis functionality. In addition to GOstats and topGO, there is also the Biocondcutor package Category, and third party tools. Martin > analysis tools in GSEABase. And what is the result of GSEA pathway analysis. > Anyone can help me. > Best, > Chunjiang > > [[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 -- 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

Hi Jiang, Please keep posts on-list, so all can benefit (and clarify) our exchange. topGO, GOstats, and PGSEA (forgot to mention that, sorry) all do variations of 'discrete' gene set analysis, comparing a list of 'selected' genes with a 'universe' of genes. To use GOstats and topGO, you would need to augment your 'selected' genes (below) with a universe of genes; how you specify the universe has been covered on this mailing list before; it is often a subset of the genes represented on the array you've used to identify interesting genes. I do not have an easy answer for how to start a Category analysis. The analysis outlined in the Category vignette requires in addition the expression values, or at least relevant t-statistics, summarizing the differential expression that you are interested in. The vignette is not a 'recipe' that you can follow line-by-line, but rather an outline of the conceptual steps that can be taken. The essence of the approach begins on p. 3, where a matrix of expression values is assessed for differential expression, probes are mapped to pathways, and differential expression is summarized per-path. Both types of analysis require some level of understanding of how Biocondcutor works. Martin chunjiang he wrote: > I have a gene id list like: > 27 > 97 > 104 > 273 > 287 > 355 > 361 > 382 > 387 > 411 > 517 > 538 > 577 > > or gene symbol list like: > C9orf152 > FSTL1 > CREB3L1 > PNMA1 > RIT2 > SLC18A1 > CD44 > PCDHB15 > FARP1 > TMEM216 > KCNMA1 > C10orf90 > C9orf39 > ZHX3 > TUBD1 > > And if I want to start the Category analysis, how could I do. I see the > introduction of Category, but it is based on ALL data. So how could I > start with my data. > Thanks very much > > Best, > Jiang > On Fri, May 22, 2009 at 11:12 AM, chunjiang he <camelbbs at="" gmail.com=""> <mailto:camelbbs at="" gmail.com="">> wrote: > > Thanks so much. > And does the result of Category is similar to GOstats or topGO. > I want to know if there is need to use Category for my work. > Best, > Jiang > > On Fri, May 22, 2009 at 10:38 AM, Martin Morgan <mtmorgan at="" fhcrc.org=""> <mailto:mtmorgan at="" fhcrc.org="">> wrote: > > chunjiang he wrote: > > hi all, > I have used GOstats and topGO to get the GO anotations of my > Gene list. Now > I hear about GSEABase can do more things about pathway > analysis. I installed > the GSEABase packages and study it. But I think I can't get > the pathway > > > GSEABase provides classes for organizing gene sets, and for > accessing gene sets available in other locations (such as those > at the Broad). It does not provide gene set analysis > functionality. In addition to GOstats and topGO, there is also > the Biocondcutor package Category, and third party tools. > > Martin > > analysis tools in GSEABase. And what is the result of GSEA > pathway analysis. > Anyone can help me. > Best, > Chunjiang > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > <mailto: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 > > > -- 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

GSEABase is infrastructure for enumerating pathways and their contents and facilitating translations among the different nomenclatures that are used to describe contents of pathways. GSEABase does not perform pathway analysis per se -- thus the "Base". On Fri, May 22, 2009 at 11:23 AM, chunjiang he <camelbbs@gmail.com> wrote: > hi all, > I have used GOstats and topGO to get the GO anotations of my Gene list. Now > I hear about GSEABase can do more things about pathway analysis. I > installed > the GSEABase packages and study it. But I think I can't get the pathway > analysis tools in GSEABase. And what is the result of GSEA pathway > analysis. > Anyone can help me. > Best, > Chunjiang > > [[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 > -- Vincent Carey, PhD Biostatistics, Channing Lab 617 525 2265 [[alternative HTML version deleted]]