On Wed, Mar 17, 2010 at 3:50 AM, neeraj rana <kushrn at="" gmail.com=""> wrote: > hi > > i install the R package R.2.10.0 for windows.And then i tried to install > bioconductor package ,but it is not installing.It's showing this error > >> source("http://bioconductor.org/biocLite.R") > Error in file(file, "r", encoding = encoding) : > ? cannot open the connection > In addition: Warning message: > In file(file, "r", encoding = encoding) : > ? unable to connect to 'bioconductor.org' on port 80. Hi, Neeraj. Are you behind a firewall? Is your network connection working? Sean > On Tue, Mar 16, 2010 at 4:06 PM, Sean Davis <seandavi at="" gmail.com=""> wrote: >> >> On Tue, Mar 16, 2010 at 6:24 AM, neeraj rana <kushrn at="" gmail.com=""> wrote: >> > hi, >> > >> > i need to analyse Agilent microrna microarray by the package AgiMicroRna >> > ,i >> > tried it to intstall but the msz ?came >> > >> >> source("http://bioconductor.org/biocLite.R") >> > Warning messages: >> > 1: In safeSource() : Redefining ?biocinstall? >> > 2: In safeSource() : Redefining ?biocinstallPkgGroups? >> > 3: In safeSource() : Redefining ?biocinstallRepos? >> >> ? ? biocLite("AgiMicroRna") >> > Using R version 2.9.2, biocinstall version 2.4.13. >> > Installing Bioconductor version 2.4 packages: >> > [1] "AgiMicroRna" >> > Please wait... >> > >> > Warning message: >> > In getDependencies(pkgs, dependencies, available, lib) : >> > ?package ?AgiMicroRna? is not available >> > >> > Please let me know whethr it is available or not,or any alternative ?? >> >> Hi, Neeraj. >> >> AgiMicroRna became available only in Bioconductor 2.5, which >> corresponds to R-2.10. ?You will need to upgrade your R to the newest >> version in order to use AgiMicroRna. >> >> Sean > >

On Wed, Mar 17, 2010 at 5:17 AM, neeraj rana <kushrn at="" gmail.com=""> wrote: > > hi sean, > > the internet is working,and i turned off the firewall also..but still i am > facing the same the problems. Hi, Neeraj. Please keep replies on the list so that you can get the best help possible. Turning off your computer firewall is not likely to solve a problem if you are behind a corporate firewall. You may need to get a local administrator to help there, as I think the bioconductor site is up right now. Sean > On Wed, Mar 17, 2010 at 2:40 PM, Sean Davis <seandavi at="" gmail.com=""> wrote: >> >> On Wed, Mar 17, 2010 at 3:50 AM, neeraj rana <kushrn at="" gmail.com=""> wrote: >> > hi >> > >> > i install the R package R.2.10.0 for windows.And then i tried to install >> > bioconductor package ,but it is not installing.It's showing this error >> > >> >> source("http://bioconductor.org/biocLite.R") >> > Error in file(file, "r", encoding = encoding) : >> > ? cannot open the connection >> > In addition: Warning message: >> > In file(file, "r", encoding = encoding) : >> > ? unable to connect to 'bioconductor.org' on port 80. >> >> Hi, Neeraj. >> >> Are you behind a firewall? ?Is your network connection working? >> >> Sean >> >> > On Tue, Mar 16, 2010 at 4:06 PM, Sean Davis <seandavi at="" gmail.com=""> wrote: >> >> >> >> On Tue, Mar 16, 2010 at 6:24 AM, neeraj rana <kushrn at="" gmail.com=""> wrote: >> >> > hi, >> >> > >> >> > i need to analyse Agilent microrna microarray by the package >> >> > AgiMicroRna >> >> > ,i >> >> > tried it to intstall but the msz ?came >> >> > >> >> >> source("http://bioconductor.org/biocLite.R") >> >> > Warning messages: >> >> > 1: In safeSource() : Redefining ?biocinstall? >> >> > 2: In safeSource() : Redefining ?biocinstallPkgGroups? >> >> > 3: In safeSource() : Redefining ?biocinstallRepos? >> >> >> ? ? biocLite("AgiMicroRna") >> >> > Using R version 2.9.2, biocinstall version 2.4.13. >> >> > Installing Bioconductor version 2.4 packages: >> >> > [1] "AgiMicroRna" >> >> > Please wait... >> >> > >> >> > Warning message: >> >> > In getDependencies(pkgs, dependencies, available, lib) : >> >> > ?package ?AgiMicroRna? is not available >> >> > >> >> > Please let me know whethr it is available or not,or any alternative >> >> > ?? >> >> >> >> Hi, Neeraj. >> >> >> >> AgiMicroRna became available only in Bioconductor 2.5, which >> >> corresponds to R-2.10. ?You will need to upgrade your R to the newest >> >> version in order to use AgiMicroRna. >> >> >> >> Sean >> > >> > > >

Dear all, i'm newbie in reading agilent 44k arrays. this is my targets file: "SlideNumber" "FileNameCy3" "FileNameCy5" "Cy3" "Cy5" 1 "prova01.txt" "prova02.txt" "WT" "Mutant" 2 "prova03.txt" "prova04.txt" "WT" "Mutant" 3 "prova05.txt" "prova06.txt" "WT" "Mutant" but readin in the limma user guide i'm not able to read the 6 chip > library("limma") > targets <- readTargets() > targets SlideNumber FileNameCy3 FileNameCy5 Cy3 Cy5 1 1 prova01.txt prova02.txt WT Mutant 2 2 prova03.txt prova04.txt WT Mutant 3 3 prova05.txt prova06.txt WT Mutant > files <- targets[,c("FileNameCy3","FileNameCy5")] > files FileNameCy3 FileNameCy5 1 prova01.txt prova02.txt 2 prova03.txt prova04.txt 3 prova05.txt prova06.txt > RG <- read.maimages(files, source="imagene") Read header information Error in read.imagene(files = files, path = path, ext = ext, names = names, : Can't find Field Dimensions in ImaGene header In addition: Warning message: In readImaGeneHeader(fullname) : End of file encountered before End Header i know that "imagene" is not correct because i have used agilent Microarray Scanner (G2565CA) so i have the 6 txt files like the one that i have attached in the mail. is there anyone that can help me in reading this kind of microarrays? Best regards. ---------------------------------------- Alberto Goldoni, PhD IT Lan Manager Medical Genetics Unit S. Orsola-Malpighi Hospital Via Massarenti n.9, Pad 11 40100 Bologna, Italy ---------------------------------------- [[alternative HTML version deleted]]