Question: using GSEAlm with GO geneSetCollections
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gravatar for Mark W Kimpel
10.5 years ago by
Mark W Kimpel830
Mark W Kimpel830 wrote:
I'm using a specific Affy chipset that is supported by BioC (rat2302) and would like to use GSEAlm to indentify GO genesets of interest (p <0.05). I am only interested in the GO BP ontology and only want to use the terminal leaves. What is the most straightforward way to achieve this? I've read the vignettes from GSEABase, GSEAlm, Category, and goTools and can't find a direct example. I suspect I am making this too hard. Suggestions? Point me in the correct direction? Thanks, Mark ------------------------------------------------------------ Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 399-1219 Home Skype: mkimpel "The real problem is not whether machines think but whether men do." -- B. F. Skinner ****************************************************************** [[alternative HTML version deleted]]
ADD COMMENTlink modified 10.5 years ago by Dykema, Karl90 • written 10.5 years ago by Mark W Kimpel830
Answer: using GSEAlm with GO geneSetCollections
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gravatar for rgentleman
10.5 years ago by
rgentleman5.5k
United States
rgentleman5.5k wrote:
Hi Mark, There is no direct way to do that (at least not that I can think of). Perhaps the easiest thing to do, is to do an unconditional test, with no filtering on p-values (or anything else). Then separately find all leaves, and then just subset the results for the leaves and work off of that. best wishes Robert Mark Kimpel wrote: > I'm using a specific Affy chipset that is supported by BioC (rat2302) and > would like to use GSEAlm to indentify GO genesets of interest (p <0.05). I > am only interested in the GO BP ontology and only want to use the terminal > leaves. What is the most straightforward way to achieve this? I've read the > vignettes from GSEABase, GSEAlm, Category, and goTools and can't find a > direct example. I suspect I am making this too hard. Suggestions? Point me > in the correct direction? > > Thanks, > Mark > ------------------------------------------------------------ > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry > Indiana University School of Medicine > > 15032 Hunter Court, Westfield, IN 46074 > > (317) 490-5129 Work, & Mobile & VoiceMail > (317) 399-1219 Home > Skype: mkimpel > > "The real problem is not whether machines think but whether men do." -- B. > F. Skinner > ****************************************************************** > > [[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, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
ADD COMMENTlink written 10.5 years ago by rgentleman5.5k
Answer: using GSEAlm with GO geneSetCollections
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gravatar for Dykema, Karl
10.5 years ago by
Dykema, Karl90
Dykema, Karl90 wrote:
Hello Mark, You may want to try PGSEA together with limma. It takes a slightly different approach than Category but this vignette should explain things adequately. http://www.bioconductor.org/packages/release/bioc/vignettes/PGSEA/inst /doc/PGSEA2.pdf ------------------------------------------- Karl Dykema Computational Biologist Van Andel Research Institute 333 Bostwick Ave NE Grand Rapids, MI 49503 Date: Mon, 10 Nov 2008 20:49:42 -0500 From: "Mark Kimpel" <mwkimpel@gmail.com> Subject: [BioC] using GSEAlm with GO geneSetCollections To: "Bioconductor Newsgroup" <bioconductor at="" stat.math.ethz.ch=""> Message-ID: <6b93d1830811101749k241749ddr62424a5e511a0c16 at mail.gmail.com> Content-Type: text/plain I'm using a specific Affy chipset that is supported by BioC (rat2302) and would like to use GSEAlm to indentify GO genesets of interest (p <0.05). I am only interested in the GO BP ontology and only want to use the terminal leaves. What is the most straightforward way to achieve this? I've read the vignettes from GSEABase, GSEAlm, Category, and goTools and can't find a direct example. I suspect I am making this too hard. Suggestions? Point me in the correct direction? Thanks, Mark This email message, including any attachments, is for th...{{dropped:6}}
ADD COMMENTlink written 10.5 years ago by Dykema, Karl90
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