Reg: GSEA

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Rohit Farmer ▴ 170

@rohit-farmer-3954

Last seen 10.2 years ago

Hello everyone ... I just did a moderate t statistics using limma package and found out a list of genes which are differentially expressed now i wan to go for gene set enrichment analysis using GO terms and pathway analysis ... so can anyone suggest me the bioconductor packages which i can use for the same .. Thanks and regards Rohit -- Rohit Farmer M.Tech Bioinformatics Department of Computational Biology and Bioinformatics Jacob School of Biengineering and Biotechnology Sam Higginbottom Institute of Agriculture, Technology and Sciences (Formerly known as Allahabad Agricultural Institute - Deemed University) Allahabad, UP, INDIA - 211 007 Ph. No. 9839845093, 9415261403 e-Mail rohit.farmer at gmail.com Blog http://rohitsspace.blogspot.com

GO limma GO limma • 1.4k views

ADD COMMENT • link updated 14.6 years ago by Saroj K Mohapatra ▴ 400 • written 14.6 years ago by Rohit Farmer ▴ 170

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Andreia Fonseca ▴ 810

@andreia-fonseca-3796

Last seen 7.8 years ago

Dear Farmer, you can use GOstats package. regards, Andreia On Mon, Apr 19, 2010 at 10:59 AM, Rohit Farmer <rohit.farmer@gmail.com>wrote: > Hello everyone ... > > I just did a moderate t statistics using limma package and found out a > list of genes which are differentially expressed now i wan to go for > gene set enrichment analysis using GO terms and pathway analysis ... > so can anyone suggest me the bioconductor packages which i can use for > the same .. > > Thanks and regards > > Rohit > -- > Rohit Farmer > M.Tech Bioinformatics > Department of Computational Biology and Bioinformatics > Jacob School of Biengineering and Biotechnology > Sam Higginbottom Institute of Agriculture, Technology and Sciences > (Formerly known as Allahabad Agricultural Institute - Deemed University) > Allahabad, UP, INDIA - 211 007 > Ph. No. 9839845093, 9415261403 > e-Mail rohit.farmer@gmail.com > Blog http://rohitsspace.blogspot.com > > _______________________________________________ > 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 > -- -------------------------------------------- Andreia J. Amaral Unidade de Imunologia Clínica Instituto de Medicina Molecular Universidade de Lisboa email: andreiaamaral@fm.ul.pt andreia.fonseca@gmail.com [[alternative HTML version deleted]]

ADD COMMENT • link 14.6 years ago Andreia Fonseca ▴ 810

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Thanks Andreia ... This GOstats package will also work with KEGG database pathway data or i have to use another package and there is one more package i found that is GSEAbase ... so which one is better or can say easy to use and implement ... Thanks rohit On 4/19/10, Andreia Fonseca <andreia.fonseca at="" gmail.com=""> wrote: > Dear Farmer, > > you can use GOstats package. > regards, > Andreia > > On Mon, Apr 19, 2010 at 10:59 AM, Rohit Farmer > <rohit.farmer at="" gmail.com="">wrote: > >> Hello everyone ... >> >> I just did a moderate t statistics using limma package and found out a >> list of genes which are differentially expressed now i wan to go for >> gene set enrichment analysis using GO terms and pathway analysis ... >> so can anyone suggest me the bioconductor packages which i can use for >> the same .. >> >> Thanks and regards >> >> Rohit >> -- >> Rohit Farmer >> M.Tech Bioinformatics >> Department of Computational Biology and Bioinformatics >> Jacob School of Biengineering and Biotechnology >> Sam Higginbottom Institute of Agriculture, Technology and Sciences >> (Formerly known as Allahabad Agricultural Institute - Deemed University) >> Allahabad, UP, INDIA - 211 007 >> Ph. No. 9839845093, 9415261403 >> e-Mail rohit.farmer at gmail.com >> Blog http://rohitsspace.blogspot.com >> >> _______________________________________________ >> 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 >> > > > > -- > -------------------------------------------- > Andreia J. Amaral > Unidade de Imunologia Cl?nica > Instituto de Medicina Molecular > Universidade de Lisboa > email: andreiaamaral at fm.ul.pt > andreia.fonseca at gmail.com > -- Rohit Farmer M.Tech Bioinformatics Department of Computational Biology and Bioinformatics Jacob School of Biengineering and Biotechnology Sam Higginbottom Institute of Agriculture, Technology and Sciences (Formerly known as Allahabad Agricultural Institute - Deemed University) Allahabad, UP, INDIA - 211 007 Ph. No. 9839845093, 9415261403 e-Mail rohit.farmer at gmail.com Blog http://rohitsspace.blogspot.com

ADD REPLY • link 14.6 years ago Rohit Farmer ▴ 170

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Hi Rohit, Yes. You can definitely test KEGG terms. But be sure you have the very latest version of the Category package. In the current release this would be 2.12.1 Marc On 04/19/2010 03:12 AM, Rohit Farmer wrote: > Thanks Andreia ... > > This GOstats package will also work with KEGG database pathway data or > i have to use another package and there is one more package i found > that is GSEAbase ... so which one is better or can say easy to use and > implement ... > > Thanks > > rohit > > On 4/19/10, Andreia Fonseca <andreia.fonseca at="" gmail.com=""> wrote: > >> Dear Farmer, >> >> you can use GOstats package. >> regards, >> Andreia >> >> On Mon, Apr 19, 2010 at 10:59 AM, Rohit Farmer >> <rohit.farmer at="" gmail.com="">wrote: >> >> >>> Hello everyone ... >>> >>> I just did a moderate t statistics using limma package and found out a >>> list of genes which are differentially expressed now i wan to go for >>> gene set enrichment analysis using GO terms and pathway analysis ... >>> so can anyone suggest me the bioconductor packages which i can use for >>> the same .. >>> >>> Thanks and regards >>> >>> Rohit >>> -- >>> Rohit Farmer >>> M.Tech Bioinformatics >>> Department of Computational Biology and Bioinformatics >>> Jacob School of Biengineering and Biotechnology >>> Sam Higginbottom Institute of Agriculture, Technology and Sciences >>> (Formerly known as Allahabad Agricultural Institute - Deemed University) >>> Allahabad, UP, INDIA - 211 007 >>> Ph. No. 9839845093, 9415261403 >>> e-Mail rohit.farmer at gmail.com >>> Blog http://rohitsspace.blogspot.com >>> >>> _______________________________________________ >>> 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 >>> >>> >> >> -- >> -------------------------------------------- >> Andreia J. Amaral >> Unidade de Imunologia Cl?nica >> Instituto de Medicina Molecular >> Universidade de Lisboa >> email: andreiaamaral at fm.ul.pt >> andreia.fonseca at gmail.com >> >> >

ADD REPLY • link 14.6 years ago Marc Carlson ★ 7.2k

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Saroj K Mohapatra ▴ 400

@saroj-k-mohapatra-3419

Last seen 10.2 years ago

Hi Rohit: Using the GOstats you can test for both over and under representation of GO terms using Hypergeometric test. There is a vignette "How To Use GOstats Testing Gene Lists for GO Term Association". Best wishes, Saroj Rohit Farmer wrote: > Hello everyone ... > > I just did a moderate t statistics using limma package and found out a > list of genes which are differentially expressed now i wan to go for > gene set enrichment analysis using GO terms and pathway analysis ... > so can anyone suggest me the bioconductor packages which i can use for > the same .. > > Thanks and regards > > Rohit >

ADD COMMENT • link 14.6 years ago Saroj K Mohapatra ▴ 400

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