There are several issues here. First, you are describing problems installing Bioconductor software that relate to your internet connectivity and have nothing to do with Bioconductor. Error in download.file(url, destfile, method, mode = "wb", ...) : cannot open URL ' that indicates a general problem that may be avoided by starting R with an --internet2 switch, but you should talk to a systems support person there to get advice relevant to your setup. Second, you are asking about exon array analysis, and there are several approaches available. The "documentation" tab of the Bioconductor web site shows a "workflows" node, and this takes you to http://www.bioconductor.org/docs/workflows/oligoarrays/ where the main options are described. That page may need a little updating as exonmap has been replaced by xmapcore (yes, the xmapcore primer refers to exonmap as deprecated). The xps system will require installation of CERN ROOT infrastructure. The oligo approach may have the lightest external infrastructure requirements and a focused analysis illustration is given in the overview vignette http://www.bioconductor.org/packages/2.6/bioc/vignettes/oligo/inst/doc /V1Overview.pdf Section 3 in particular takes you through the import and preprocessing of some exon arrays (that you must download yourself from affymetrix), all the way to visualizing expression patterns over a gene model for a specific gene; the workflow involves biomaRt, annotationDbi, Biostrings, and GenomeGraphs. I would suggest that exon array analysis is not an activity with which one should START using bioconductor. IMHO, mastery of general issues with array import and quality assessment, general tasks of annotation and identifier resolution, and statistics of differential expression at the gene level should be acquired before getting involved with exon arrays. On Wed, May 26, 2010 at 3:00 AM, l.mohammadikhankahdani < l.mohammadikhankahdani@erasmusmc.nl> wrote: > > Does anyone have experience with exon array analysis? > If so, do you know how to install huex10stv2cdf package? > > best > Leila > > > > on 2010/05/26 10:38 AM mahalakshmi sivamani said the following: > >> Hi, >> >> While trying to install hgu133acdf- windows package in R i am getting the >> following error and unable to install the same. >> >> source("http://bioconductor.org/biocLite.R") >>> biocLite("hgu133acdf") >>> >> Using R version 2.10.0, biocinstall version 2.5.10. >> Installing Bioconductor version 2.5 packages: >> [1] "hgu133acdf" >> Please wait... >> >> trying URL ' >> >> http://www.bioconductor.org/packages/2.5/data/annotation/bin/window s/contrib/2.10/hgu133acdf_2.5.0.zip >> ' >> Error in download.file(url, destfile, method, mode = "wb", ...) : >> cannot open URL ' >> >> http://www.bioconductor.org/packages/2.5/data/annotation/bin/window s/contrib/2.10/hgu133acdf_2.5.0.zip >> ' >> In addition: Warning message: >> In download.file(url, destfile, method, mode = "wb", ...) : >> cannot open: HTTP status was '0 (nil)' >> Warning in download.packages(pkgs, destdir = tmpd, available = available, >> : >> download of package 'hgu133acdf' failed >> >> Is there any possibilities of getting out from this problem. >> >> Please do the needful. Thanks in advance. >> >> Regards, >> >> S.Mahalakshmi >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 >> > > _______________________________________________ > 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]]

Hi Leila, Please stop hijacking existing threads. If you want to ask a question, send a new email to bioconductor at stat.math.ethz.ch rather than taking an existing email, changing the subject and replying to all. Best, Jim l.mohammadikhankahdani wrote: > > Does anyone have experience with exon array analysis? > If so, do you know how to install huex10stv2cdf package? > > best > Leila > > > > on 2010/05/26 10:38 AM mahalakshmi sivamani said the following: >> Hi, >> >> While trying to install hgu133acdf- windows package in R i am getting the >> following error and unable to install the same. >> >>> source("http://bioconductor.org/biocLite.R") >>> biocLite("hgu133acdf") >> Using R version 2.10.0, biocinstall version 2.5.10. >> Installing Bioconductor version 2.5 packages: >> [1] "hgu133acdf" >> Please wait... >> >> trying URL ' >> http://www.bioconductor.org/packages/2.5/data/annotation/bin/window s/contrib/2.10/hgu133acdf_2.5.0.zip >> >> ' >> Error in download.file(url, destfile, method, mode = "wb", ...) : >> cannot open URL ' >> http://www.bioconductor.org/packages/2.5/data/annotation/bin/window s/contrib/2.10/hgu133acdf_2.5.0.zip >> >> ' >> In addition: Warning message: >> In download.file(url, destfile, method, mode = "wb", ...) : >> cannot open: HTTP status was '0 (nil)' >> Warning in download.packages(pkgs, destdir = tmpd, available = >> available, : >> download of package 'hgu133acdf' failed >> >> Is there any possibilities of getting out from this problem. >> >> Please do the needful. Thanks in advance. >> >> Regards, >> >> S.Mahalakshmi >> >> [[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 > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues