Dear michael: Thanks for your help. I am testing this package. It seems need to recompile with new version of R. This is what I got. >library(CORNA) Loading required package: biomaRt Loading required package: GEOquery Loading required package: RCurl Attaching package: 'GEOquery' The following object(s) are masked from package:Biostrings : dataTable Loading required package: XML Warning message: package 'CORNA' was built under R version c(2, 4, 0) and help will not work correctly Please re-install it Weihsin Wang, Ph.D. Bioinformatics Core Lab., Biomedical Engineering Research Lab., Industrial Technology Research Institute TEL:886-3-5913689 FAX: 886-3-5820445 ________________________________________ ???: bioconductor-bounces at stat.math.ethz.ch [bioconductor-bounces at stat.math.ethz.ch] ?? michael watson (IAH-C) [michael.watson at bbsrc.ac.uk] ????: 2010?02?26? ?? 04:26 ???: 'Laurent Gautier'; bioconductor at stat.math.ethz.ch ??: Re: [BioC] pair information of microRNA and Targets prediction Hi We published an R package early in 2009 which may help you: http://bioinformatics.iah.ac.uk/software/corna Wu X, Watson M: CORNA: testing gene lists for regulation by microRNAs. Bioinformatics 2009, 25(6):832-833. CORNA can download data directly from miRBase targets (now called Microcosm targets) but this hasn't been updated in a while. CORNA can, though, take any generic list of miR:gene target pairs and use that instead. Thanks Mick Watson Head of Bioinformatics Institute for Animal Health -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor- bounces@stat.math.ethz.ch] On Behalf Of Laurent Gautier Sent: 26 February 2010 08:20 To: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] pair information of microRNA and Targets prediction Hi Weihsin, My understanding is that microRNA only contains example data (so the exact version for the data source is of moderate importance). The only package containing database data might be "RmiR.Hs.miRNA" (dependency of RmiR). The version might be indicated in the source code (check the SVN repository for that bioconductor package), otherwise the author should be contacted. Laurent On 2/26/10 11:34 AM, jrwang at itri.org.tw wrote: > > I am currently working on some microRNA experiments. I would like to > find the relation between microRNA and predicted targets from > targetscan and miRanda. To do it from scratch will be last choice. I > look the currently available packages. Two packages, RmiR and > microRNA, seems fitting my purpose. However, there are a few > questions after I use the packages. 1. What is the version of mirbase > used in most current microRNA package? 2. Similar to question 1, > what is the version of data from various resources used in RmiR? Is > there a way to find out? > > Thanks > >> sessionInfo() > R version 2.10.1 (2009-12-14) i386-pc-mingw32 > > locale: [1] LC_COLLATE=Chinese_Taiwan.950 > LC_CTYPE=Chinese_Taiwan.950 LC_MONETARY=Chinese_Taiwan.950 > LC_NUMERIC=C LC_TIME=Chinese_Taiwan.950 > > attached base packages: [1] stats graphics grDevices utils > datasets methods base > > other attached packages: [1] microRNA_1.4.0 Rlibstree_0.3-2 > Biostrings_2.14.12 IRanges_1.4.11 RmiR_1.2.0 > RSVGTipsDevice_1.0-1 RmiR.Hs.miRNA_1.0.6 RSQLite_0.8-3 > DBI_0.2-5 > > loaded via a namespace (and not attached): [1] AnnotationDbi_1.8.1 > Biobase_2.6.1 > > > Weihsin Wang, Ph.D. Bioinformatics Core Lab., Biomedical Engineering > Research Lab., Industrial Technology Research Institute > TEL:886-3-5913689 FAX: 886-3-5820445 > > ???????????????????????????????????????????? This email may contain > confidential information. Please do not use or disclose it in any way > and delete it if you are not the intended recipient. > _______________________________________________ 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 _______________________________________________ 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 ???????????????????????????????????????????? This email may contain confidential information. Please do not use or disclose it in any way and delete it if you are not the intended recipient.