How can i download the eset available on ncbi through this command gset <- getGEO("GSE1542", GSEMatrix =TRUE) -- output of sessionInfo(): >library(GEOquery) Loading required package: Biobase Loading required package: BiocGenerics Attaching package: ???BiocGenerics??? The following object(s) are masked from ???package:stats???: xtabs The following object(s) are masked from ???package:base???: anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Setting options('download.file.method.GEOquery'='auto')>gset <- getGEO("GSE1542", GSEMatrix =TRUE) Error in function (type, msg, asError = TRUE) : Could not resolve host: ftp.ncbi.nlm.nih.gov; No data record of requested type > traceback() 7: fun(structure(list(message = msg, call = sys.call()), class = c(typeName, "GenericCurlError", "error", "condition"))) 6: function (type, msg, asError = TRUE) { if (!is.character(type)) { i = match(type, CURLcodeValues) typeName = if is.na(i)) character() else names(CURLcodeValues)[i] } typeName = gsub("^CURLE_", "", typeName) fun = (if (asError) stop else warning) fun(structure(list(message = msg, call = sys.call()), class = c(typeName, "GenericCurlError", "error", "condition"))) }(6L, "Could not resolve host: ftp.ncbi.nlm.nih.gov; No data record of requested type", TRUE) 5: .Call("R_curl_easy_perform", curl, .opts, isProtected, .encoding, PACKAGE = "RCurl") 4: curlPerform(curl = curl, .opts = opts, .encoding = .encoding) 3: getURL(sprintf("ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/SeriesMatri x/%s/", GEO)) 2: getAndParseGSEMatrices(GEO, destdir, AnnotGPL = AnnotGPL) 1: getGEO("GSE1542", GSEMatrix = TRUE) > sessionInfo() -- Sent via the guest posting facility at bioconductor.org.

On Wed, Oct 17, 2012 at 5:06 AM, T.Kartheeswaran [guest] < guest@bioconductor.org> wrote: > > How can i download the eset available on ncbi through this command > gset <- getGEO("GSE1542", GSEMatrix =TRUE) > > > > > -- output of sessionInfo(): > > >library(GEOquery) > Loading required package: Biobase > Loading required package: BiocGenerics > > Attaching package: ‘BiocGenerics’ > > The following object(s) are masked from ‘package:stats’: > > xtabs > > The following object(s) are masked from ‘package:base’: > > anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, > get, intersect, lapply, Map, mapply, mget, order, paste, pmax, > pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, > rownames, sapply, setdiff, table, tapply, union, unique > > Welcome to Bioconductor > > Vignettes contain introductory material; view with > 'browseVignettes()'. To cite Bioconductor, see > 'citation("Biobase")', and for packages 'citation("pkgname")'. > > Setting options('download.file.method.GEOquery'='auto')>gset <- > getGEO("GSE1542", GSEMatrix =TRUE) > Error in function (type, msg, asError = TRUE) : > Could not resolve host: ftp.ncbi.nlm.nih.gov; No data record of > requested type > Obvious question, but are you connected to the internet? If so, are you behind a firewall? If you are behind a firewall, do you need to set up a proxy? Sean > > traceback() > 7: fun(structure(list(message = msg, call = sys.call()), class = > c(typeName, > "GenericCurlError", "error", "condition"))) > 6: function (type, msg, asError = TRUE) > { > if (!is.character(type)) { > i = match(type, CURLcodeValues) > typeName = if is.na(i)) > character() > else names(CURLcodeValues)[i] > } > typeName = gsub("^CURLE_", "", typeName) > fun = (if (asError) > stop > else warning) > fun(structure(list(message = msg, call = sys.call()), class = > c(typeName, > "GenericCurlError", "error", "condition"))) > }(6L, "Could not resolve host: ftp.ncbi.nlm.nih.gov; No data record of > requested type", > TRUE) > 5: .Call("R_curl_easy_perform", curl, .opts, isProtected, .encoding, > PACKAGE = "RCurl") > 4: curlPerform(curl = curl, .opts = opts, .encoding = .encoding) > 3: getURL(sprintf(" > ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/SeriesMatrix/%s/", > GEO)) > 2: getAndParseGSEMatrices(GEO, destdir, AnnotGPL = AnnotGPL) > 1: getGEO("GSE1542", GSEMatrix = TRUE) > > > sessionInfo() > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]