Pete Does following the link from here: http://www.nature.com/nature/journal/v456/n7221/full/nature07509.html to here http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12946 give you what you want? Cheers Richard Martin Morgan wrote: > Pete Shepard <peter.shepard at="" gmail.com=""> writes: > >> Dear List, >> >> Does anyone know if the sequences generated using mrna seq protocol fro Wang >> and Burge Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, >> Kingsmore SF, Schroth GP, Burge CB. (2008). Alternative Isoform Regulation >> in Human Tissue Transcriptomes. Nature *456,* 470-476. Full >> Text<http: www.nature.com="" nature="" journal="" v456="" n7221="" abs="" nature0750="" 9.html="">is >> piblicly available? > > Hi Pete -- > > You can visit NCBI's PubMed data base > > http://0-www.ncbi.nlm.nih.gov.millennium.unicatt.it/sites/entrez?d b=PubMed > > and search for, e.g., Burge Wang, follow the appropriate link to the > citation, then click on the 'Links' button and go to the 'GEO > Datasets' link and 'Download...' the supplementary files. You might > also have luck going to GEO directly, or to the Short Read Archive, or > visiting the paper's supplementary material for GEO and SRA accession > numbers. > > Martin > >> TIA >> >> [[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 > -- 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 287575 Roosevelt Drive Mob: +44 (0)7971 221181 Oxford OX3 7BN, UK Fax: +44 (0)1865 287664

Hi, I suspect you are having a problem with the proxy server / firewall settings at your system. I was able to install the package without any problem (see below). Best wishes, Saroj > library("hthgu133acdf") Error in library("hthgu133acdf") : there is no package called 'hthgu133acdf' > > source("http://www.bioconductor.org/biocLite.R") > biocLite("hthgu133acdf") Running biocinstall version 2.4.10 with R version 2.9.0 Your version of R requires version 2.4 of Bioconductor. trying URL 'http://bioconductor.org/packages/2.4/data/annotation/src/contrib/hth gu133acdf_2.4.0.tar.gz' Content type 'application/x-gzip' length 1738820 bytes (1.7 Mb) opened URL ================================================== downloaded 1.7 Mb * Installing *source* package ?hthgu133acdf? ... ** R ** data ** preparing package for lazy loading ** help *** installing help indices >>> Building/Updating help pages for package 'hthgu133acdf' Formats: text html latex example geometry text html latex example hthgu133acdf text html latex hthgu133adim text html latex ** building package indices ... * DONE (hthgu133acdf) The downloaded packages are in ?/tmp/RtmpH6JhO7/downloaded_packages? Updating HTML index of packages in '.Library' > library("hthgu133acdf") > sessionInfo() R version 2.9.0 (2009-04-17) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_ MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_A DDRESS=C;L C_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.9.0 ??? wrote: > Dear Sir: > > I encounter difficulty in downloading hthgu133acdf_2.4.0.zip through > following R code > source("http://bioconductor.org/biocLite.R") > biocLite("hthgu133acdf") > > Could you solve this problem? Thanks > > >

Chueh-Chuan, Telling more about your R version and bioconductor version will help people to help you, and so does the exact error message you are having. (check: http://www.bioconductor.org/docs/postingGuide.html) Your mention of a .zip makes me think that you are MS Windows based, and all I can tell is that the package is available http://bioconductor.org/packages/2.4/data/annotation/html/hthgu133acdf .html and that it is working with Linux. > source("http://bioconductor.org/biocLite.R") > biocLite("hthgu133acdf") Running biocinstall version 2.4.10 with R version 2.9.0 Your version of R requires version 2.4 of Bioconductor. trying URL 'http://bioconductor.org/packages/2.4/data/annotation/src/contrib/hthg u133acdf_2.4.0.tar.gz' Content type 'application/x-gzip' length 1738820 bytes (1.7 Mb) opened URL ================================================== downloaded 1.7 Mb * Installing *source* package ?hthgu133acdf? ... ** R ** data ** preparing package for lazy loading ** help *** installing help indices >>> Building/Updating help pages for package 'hthgu133acdf' Formats: text html latex example geometry text html latex example hthgu133acdf text html latex hthgu133adim text html latex ** building package indices ... * DONE (hthgu133acdf) The downloaded packages are in ?/tmp/RtmpJB3cP1/downloaded_packages? Updating HTML index of packages in '.Library' L. -- Laurent Gautier, Ph.D. Building 301, CBS - Technical University of Denmark DK-2800 Lyngby tel: +45 45 25 61 45 On Sat, 2009-05-02 at 23:27 +0800, ??? wrote: > Dear Sir: > > I encounter difficulty in downloading hthgu133acdf_2.4.0.zip through > following R code > source("http://bioconductor.org/biocLite.R") > biocLite("hthgu133acdf") > > Could you solve this problem? Thanks > >

Dear Sir: I encounter difficulty in downloading hthgu133acdf_2.4.0.zip through following R code source("http://bioconductor.org/biocLite.R") biocLite("hthgu133acdf") Could you solve this problem? Thanks Yen CC 2009/5/2 ??? <ccyen at="" vghtpe.gov.tw="">: > Dear Sir: > > I encounter difficulty in downloading hthgu133acdf_2.4.0.zip through > following R code > source("http://bioconductor.org/biocLite.R") > biocLite("hthgu133acdf") > > Could you solve this problem? Thanks > > > -- > Chueh-Chuan Yen, MD, Ph.D. > Division of Hematology & Oncology > Department of Medicine > Taipei Veterans General Hospital > NO 201, Sec 2, Shih-Pai Road, Taipei 112,Taiwan > TEL:+886-2-28712121 ext 2525 > FAX:+886-2-28732184 > -- Chueh-Chuan Yen, MD, Ph.D. Division of Hematology & Oncology Department of Medicine Taipei Veterans General Hospital NO 201, Sec 2, Shih-Pai Road, Taipei 112,Taiwan TEL:+886-2-28712121 ext 2525 FAX:+886-2-28732184