hiii, Myself Sneha... I want to discuss the error am repeatedly getting while running the GCRMA normalization and cannot solve it.Ihave installed the required HG_U95Av2 probes and CDF packages still it is giving this error.Can u please help me. > library(gcrma) > esetGCRMA <- gcrma(rawdata) Adjusting for optical effect.........Done. Computing affinitiesError in getProbePackage(probepackagename) : The current operation could not access the Bioconductor repository. Please check your internet connection, and report further problems to bioconductor@stat.math.ethz.ch > sessionInfo function (package = NULL) { z <- list() z$R.version <- R.Version() z$locale <- Sys.getlocale() if (is.null(package)) { package <- grep("^package:", search(), value = TRUE) keep <- sapply(package, function(x) x == "package:base" || !is.null(attr(as.environment(x), "path"))) package <- sub("^package:", "", package[keep]) } pkgDesc <- lapply(package, packageDescription) if (length(package) == 0) stop("no valid packages were specified") basePkgs <- sapply(pkgDesc, function(x) !is.null(x$Priority) && x$Priority == "base") z$basePkgs <- package[basePkgs] if (any(!basePkgs)) { z$otherPkgs <- pkgDesc[!basePkgs] names(z$otherPkgs) <- package[!basePkgs] } loadedOnly <- loadedNamespaces() loadedOnly <- loadedOnly[!(loadedOnly %in% package)] if (length(loadedOnly)) { names(loadedOnly) <- loadedOnly pkgDesc <- c(pkgDesc, lapply(loadedOnly, packageDescription)) z$loadedOnly <- pkgDesc[loadedOnly] } class(z) <- "sessionInfo" z } <environment: namespace:utils=""> > [[alternative HTML version deleted]]

Hi Sneha, sneha patil wrote: > hiii, > Myself Sneha... > I want to discuss the error am repeatedly getting while running the GCRMA > normalization and cannot solve it.Ihave installed the required HG_U95Av2 > probes and CDF packages still it is giving this error.Can u please help me. > > >> library(gcrma) >> esetGCRMA <- gcrma(rawdata) > Adjusting for optical effect.........Done. > Computing affinitiesError in getProbePackage(probepackagename) : > The current operation could not access the Bioconductor repository. Please > check your internet connection, and report further problems to > bioconductor at stat.math.ethz.ch > What we need here is the output from sessionInfo() (note the two parentheses). What you have given is just the function itself. And you could also give us the output from typing rawdata at the R prompt as well (after creating the AffyBatch you are calling 'rawdata'). Best, Jim >> sessionInfo > function (package = NULL) > { > z <- list() > z$R.version <- R.Version() > z$locale <- Sys.getlocale() > if (is.null(package)) { > package <- grep("^package:", search(), value = TRUE) > keep <- sapply(package, function(x) x == "package:base" || > !is.null(attr(as.environment(x), "path"))) > package <- sub("^package:", "", package[keep]) > } > pkgDesc <- lapply(package, packageDescription) > if (length(package) == 0) > stop("no valid packages were specified") > basePkgs <- sapply(pkgDesc, function(x) !is.null(x$Priority) && > x$Priority == "base") > z$basePkgs <- package[basePkgs] > if (any(!basePkgs)) { > z$otherPkgs <- pkgDesc[!basePkgs] > names(z$otherPkgs) <- package[!basePkgs] > } > loadedOnly <- loadedNamespaces() > loadedOnly <- loadedOnly[!(loadedOnly %in% package)] > if (length(loadedOnly)) { > names(loadedOnly) <- loadedOnly > pkgDesc <- c(pkgDesc, lapply(loadedOnly, packageDescription)) > z$loadedOnly <- pkgDesc[loadedOnly] > } > class(z) <- "sessionInfo" > z > } > <environment: namespace:utils=""> > > [[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 -- 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