Thank you, Marco. We will work through this material and see how it goes. best wishes, Chris On Jan 19, 2012, at 1:12 AM, Manca Marco (PATH) wrote: Dear Chris you might take advantage of the rich set of tutorials that Langfelder and Horvath have made available on their WGCNA page ( http://www.genet ics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/ ) Specifically the one entitled "Interfacing network analysis with other data such as functional annotation and gene ontology" seems to answer your needs -> http://www.genetics.ucla.edu/labs/horvath/CoexpressionNe twork/Rpackages/WGCNA/Tutorials/FemaleLiver-04-Interfacing.pdf If you have more specific doubts/questions after exploring these documents, please do not hesitate to contact our mailing list again. Best regards, Marco -- Dr Marco Manca University of Maastricht Faculty of Health, Medicine and Life Sciences (FHML) Cardiovascular Research Institute (CARIM) Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands) Visiting address: UNS40 West building - 5th floor Room5.544, Universiteit Singel 40, 6229 HX Maastricht E-mail: m.manca@maastrichtuniversity.nl<mailto:m.manca@maastrichtunive rsity.nl=""> Office telephone: +31(0)433884289 Personal mobile: +31(0)626441205 Twitter: @markomanka ********************************************************************** *********************************************** This email and any files transmitted with it are confidential and solely for the use of the intended recipient. It may contain material protected by privacy or attorney-client privilege. If you are not the intended recipient or the person responsible for delivering to the intended recipient, be advised that you have received this email in error and that any use is STRICTLY PROHIBITED. If you have received this email in error please notify us by telephone on +31626441205 Dr Marco MANCA ********************************************************************** *********************************************** ________________________________________ Da: bioconductor-bounces@r-project.org<mailto:bioconductor- bounces@r-project.org=""> [bioconductor-bounces@r-project.org<mailto :bioconductor-bounces@r-project.org="">] per conto di Christopher Gregg [guest] [guest@bioconductor.org<mailto:guest@bioconductor.org>] Inviato: mercoledì 18 gennaio 2012 23.39 A: bioconductor@r-project.org<mailto:bioconductor@r-project.org>; chris.gregg@neuro.utah.edu<mailto:chris.gregg@neuro.utah.edu> Oggetto: [BioC] how to get a list of the genes in each module in WGCNA Hi, My group has been using the WGCNA package to uncover gene modules in RNA-Seq data. We are just starting to learn the package and it is very complex. We have managed to generate the dendrogram that reveals the gene modules in a graphical format by following one of the vignettes. However, we can't figure out how to write out a file of the genes that were assigned to each of the modules. Can anyone please offer some insights on this aspect of the analysis or a vignette that takes one through these steps? Thank you very much. Sincerely, Chris -- output of sessionInfo(): R version 2.14.0 (2011-10-31) Platform: i386-apple-darwin9.8.0/i386 (32-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] annotate_1.32.0 AnnotationDbi_1.16.5 Biobase_2.14.0 DBI_0.2-5 DESeq_1.6.1 [6] genefilter_1.36.0 geneplotter_1.32.1 grid_2.14.0 IRanges_1.12.3 RColorBrewer_1.0-5 [11] RSQLite_0.10.0 splines_2.14.0 survival_2.36-10 xtable_1.6-0 -- Sent via the guest posting facility at bioconductor.org<http: bioconductor.org="">. _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org<mailto:bioconductor@r-project.org> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Christopher Gregg, PhD. New York Stem Cell Foundation-Robertson Investigator Assistant Professor, Neurobiology and Anatomy 323 Wintrobe Bldg 530 University of Utah, School of Medicine 20 North 1900 East, 401 MREB Salt Lake City, Utah 84132-3401 phone: (801) 581-8212 fax: (801) 585-9736 ------------------------------------ Gregg Lab Website: www.neuro.utah.edu/labs/gregg/index.html<http: www="" .neuro.utah.edu="" labs="" gregg="" index.html=""> [[alternative HTML version deleted]]