Reg: PCA in bioconductor
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Rohit Farmer ▴ 170
@rohit-farmer-3954
Last seen 9.6 years ago
Hello everyone ... I am using affymetrix data and want to do PCA using bioconductor ... is there any package or library available which i can use to perform the same ... Thanks 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
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@sean-davis-490
Last seen 12 weeks ago
United States
On Wed, Apr 14, 2010 at 9:17 AM, Rohit Farmer <rohit.farmer at="" gmail.com=""> wrote: > Hello everyone ... > > I am using affymetrix data and want to do PCA using bioconductor ... > is there any package or library available which i can use to perform > the same ... Hi, Rohit. The message I wrote this morning to answer your last question applies here, as well. RSiteSearch(), help(), and help.search() are very useful places to start such a seach. Sean
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@cristobal-fresno-rodriguez-3838
Last seen 7.9 years ago
Argentina/Cordoba/Universidad Católica …
Rohit, I would try ?prcomp or ?princomp from the stats package. Hope it works for you, Cristobal 2010/4/14 Rohit Farmer <rohit.farmer@gmail.com> > Hello everyone ... > > I am using affymetrix data and want to do PCA using bioconductor ... > is there any package or library available which i can use to perform > the same ... > > Thanks > > 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 > [[alternative HTML version deleted]]
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Hello, Is there a Bioconductor solution to Medline mining? Say, for a given set of affy identifiers, find gene names, their synonyms, and the pubmed count of abstracts cooccurring with a given keyword (such as a disease name)? If not available in Bioconductor, is any other tool available for this? Searches in bioinformatic journals yield only old tools which (for the most part) have dead urls. Thanks, Michael
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Hi Michael, With or without microarray data, you can use a tool called GeneMesh, which mines PubMed and based on citation statistics...it will give you genes associated with diseases, therapeutics or any other key word. GeneMesh is freely available online at: http://proteogenomics.musc.edu/genemesh/ PubMed: http://www.ncbi.nlm.nih.gov/pubmed?term=20359363 GeneMesh's distinct user interface (i.e., Web 2.0) allows users to explore the GeneMesh database in three different ways to find genes related to MeSH Terms: 1. With or without any data set, users can mine Genes related to a Search Term (e.g., stem cells, angiogenesis, etc.). 2. With or without any dataset, users can enter Entrez GeneID(s) and find related MeSH terms. 3. Users can upload gene expression data and perform analysis limited to a specific subcategory (e.g., cardiovascular diseases) or a broad category (e.g., Diseases), allowing for biased and unbiased analysis. Let me know if you have any questions, Saurin --- On Wed, 4/14/10, Michael Imbeault <michael.imbeault at="" sympatico.ca=""> wrote: > From: Michael Imbeault <michael.imbeault at="" sympatico.ca=""> > Subject: [BioC] Medline mining of microarray data (w/ synonyms and extra keyword?) > To: bioconductor at stat.math.ethz.ch > Date: Wednesday, April 14, 2010, 9:51 AM > Hello, > > Is there a Bioconductor solution to Medline mining? Say, > for a given set of affy identifiers, find gene names, their > synonyms, and the pubmed count of abstracts cooccurring with > a given keyword (such as a disease name)? > > If not available in Bioconductor, is any other tool > available for this? Searches in bioinformatic journals yield > only old tools which (for the most part) have dead urls. > > Thanks, > Michael > > _______________________________________________ > 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 >
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Hi Michael, look at org.Hs.egPMID in the org.Hs.eg.db annotation package if you are starting from NCBI Entrez Gene identifiers or the analogue extension PMID for any affy based annotation package. HTH. J. Michael Imbeault wrote: > Hello, > > Is there a Bioconductor solution to Medline mining? Say, for a given set > of affy identifiers, find gene names, their synonyms, and the pubmed > count of abstracts cooccurring with a given keyword (such as a disease > name)? > > If not available in Bioconductor, is any other tool available for this? > Searches in bioinformatic journals yield only old tools which (for the > most part) have dead urls. > > Thanks, > Michael > > _______________________________________________ > 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 >
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Hi Rohit You might also want to try 'pumaPCA' from the 'puma' package. It works on an 'ExpressionSet' object created using mmgmos (also in puma). This allows you to use uncertainty information as well as point estimates of expression levels, and can be helpful in many situations. It is more compute intensive than prcomp or princomp though! See puma vignette for further details Cheers Richard Cristobal Fresno Rodr?guez wrote: > Rohit, I would try ?prcomp or ?princomp from the stats package. > Hope it works for you, > Cristobal > > 2010/4/14 Rohit Farmer <rohit.farmer at="" gmail.com=""> > >> Hello everyone ... >> >> I am using affymetrix data and want to do PCA using bioconductor ... >> is there any package or library available which i can use to perform >> the same ... >> >> Thanks >> >> 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 >> > > [[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 > -- Dr Richard D Pearson richard.pearson at well.ox.ac.uk Wellcome Trust Centre for Human Genetics http://www.well.ox.ac.uk/~rpearson University of Oxford Tel: +44 (0)1865 617890 Roosevelt Drive Mob: +44 (0)7971 221181 Oxford OX3 7BN, UK Fax: +44 (0)1865 287664
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