Hi Peter, On 12/5/2011 9:38 AM, Peter Davidsen wrote: > Dear List, > > I'm trying to filter some microRNA expression data generated on the > Affymetrix miRNA 2.0 array platform before running the DE genes > analysis. > However, I get an error when I apply the nsFilter function in the > genefilter package - see below: > > #### my script #### > #Set working dir > setwd("C:/Users/CEL") > > #produce a character vector of the names of the files > celfiles<- list.files(path="C:/Users/CEL") > > #load packages > library(affy) > library(mirna20cdf) > > #read CEL files and compute an expression measure > exprs<- justRMA(cdfname="mirna20", normalize=TRUE) #Create a > normalized exprSet object > > exprsFiltered<- nsFilter(exprs, remove.dupEntrez=F, var.cutoff=0.5)$eset > Error: getAnnMap: package mirna20 not available > > When I tried to install the "mirna20.db" annotation file: > >> source("http://bioconductor.org/biocLite.R") > BiocInstaller version 1.2.1, ?biocLite for help > >> biocLite("mirna20.db") > BioC_mirror: 'http://www.bioconductor.org' > Using R version 2.14, BiocInstaller version 1.2.1. > Installing package(s) 'mirna20.db' > Installing package(s) into ?C:/Users/Peter > Davidsen/Documents/R/win-library/2.14? > (as ?lib? is unspecified) > Old packages: 'AnnotationDbi' > Update all/some/none? [a/s/n]: a > trying URL 'http://www.bioconductor.org/packages/2.9/bioc/bin/window s/contrib/2.14/AnnotationDbi_1.16.8.zip' > Content type 'application/zip' length 5667171 bytes (5.4 Mb) > opened URL > downloaded 5.4 Mb > > package ?AnnotationDbi? successfully unpacked and MD5 sums checked > > The downloaded packages are in > C:\Users\Peter > Davidsen\AppData\Local\Temp\RtmpWsjZYt\downloaded_packages > Warning messages: > 1: In getDependencies(pkgs, dependencies, available, lib) : > package ?mirna20.db? is not available (for R version 2.14.0) The package you want to install doesn't exist. I suppose it would be possible to create an annotation package for this chip, but not with the existing infrastructure. The miRNA2.0 chip has miRNA targets for 71 different species. In addition, each miRNA has on average 1000 different mRNA targets. So an annotation package would be really messy, and I am not sure it would be all that helpful. And think about what you would be asking with your nsfilter() call. A given miRNA can have around 1000 mRNA targets, and there are something like 1500 miRNAs for e.g., H. sapiens. Do you really want to eliminate all of them that have duplicate Entrez Gene IDs? In addition, miRNAs don't AFAIK have Entrez Gene IDs. But their targets do. So if you think about it, what you were trying to do isn't really a good idea. > 2: 'abind' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable That's a pretty clear error: it says that R doesn't have permission to write to the library directory. Windows > XP are all more Unix-like in that the permissions to do things have been seriously curtailed. You would have had to invoke administrator privileges to install R in that directory, and there may be problems installing things even if you run R as administrator. Anyway, I am not sure about the nitty-gritty details of getting R to install to the system library on newer versions of Windows, and frankly this isn't the place to ask. Your best bet is to go do a search on R-help (or google) for something like installed directory 'C:/Program Files/R/R-2.14.0/library' not writeable or some subset thereof. Best, Jim > 'acepack' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'AER' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'affy' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'affydata' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'affyio' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'affyPLM' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'affyQCReport' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'akima' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'annaffy' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0 [... truncated] > Any help would be appreciated > > > Many thanks, > Peter > > >> sessionInfo() > R version 2.14.0 (2011-10-31) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United > Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 > [4] LC_NUMERIC=C LC_TIME=English_United > Kingdom.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] genefilter_1.36.0 mirna20cdf_2.9.1 AnnotationDbi_1.16.8 > affy_1.32.0 Biobase_2.14.0 BiocInstaller_1.2.1 > > loaded via a namespace (and not attached): > [1] affyio_1.22.0 annotate_1.32.0 DBI_0.2-5 > IRanges_1.12.4 preprocessCore_1.16.0 RSQLite_0.10.0 > [7] splines_2.14.0 survival_2.36-10 tools_2.14.0 > xtable_1.6-0 zlibbioc_1.0.0 > > >> exprsFiltered<- nsFilter(exprs, remove.dupEntrez=F, var.cutoff=0.5)$eset > Error: getAnnMap: package mirna20 not available >> traceback() > 10: stop("getAnnMap: ", "package ", pkg, " not available", call. = FALSE) > 9: value[[3L]](cond) > 8: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > 7: tryCatchList(expr, classes, parentenv, handlers) > 6: tryCatch(as.environment(searchName), error = function(e) { > if (load) { > ok<- suppressWarnings(require(pkg, character.only = TRUE, > quietly = TRUE)) > if (!ok&& length(type)> 1) { > origPkg<- pkg > for (t in type[2:length(type)]) { > pkg<- annPkgName(name = chip, type = t) > searchName<- paste("package", pkg, sep = ":") > if (suppressWarnings(require(pkg, character.only = TRUE, > quietly = TRUE))) { > if (!typeMissed) > warning("getAnnMap: ", "package ", origPkg, > " not available, ", "using ", pkg, " instead", > call. = FALSE) > ok<- TRUE > break > } > } > } > if (!ok) > stop("getAnnMap: ", "package ", pkg, " not available", > call. = FALSE) > as.environment(searchName) > } > else { > stop("getAnnMap: ", pkg, " package not attached and load is FALSE", > call. = FALSE) > } > }) > 5: getAnnMap("_dbconn", chip) > 4: .findDBMeta(chip, "CENTRALID") > 3: .findCentralMap(annChip) > 2: nsFilter(exprs, remove.dupEntrez = F, var.cutoff = 0.5) > 1: nsFilter(exprs, remove.dupEntrez = F, var.cutoff = 0.5) > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > 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

Hi Peter, On 12/5/2011 9:38 AM, Peter Davidsen wrote: > Dear List, > > I'm trying to filter some microRNA expression data generated on the > Affymetrix miRNA 2.0 array platform before running the DE genes > analysis. > However, I get an error when I apply the nsFilter function in the > genefilter package - see below: > > #### my script #### > #Set working dir > setwd("C:/Users/CEL") > > #produce a character vector of the names of the files > celfiles<- list.files(path="C:/Users/CEL") > > #load packages > library(affy) > library(mirna20cdf) > > #read CEL files and compute an expression measure > exprs<- justRMA(cdfname="mirna20", normalize=TRUE) #Create a > normalized exprSet object > > exprsFiltered<- nsFilter(exprs, remove.dupEntrez=F, var.cutoff=0.5)$eset > Error: getAnnMap: package mirna20 not available > > When I tried to install the "mirna20.db" annotation file: > >> source("http://bioconductor.org/biocLite.R") > BiocInstaller version 1.2.1, ?biocLite for help > >> biocLite("mirna20.db") > BioC_mirror: 'http://www.bioconductor.org' > Using R version 2.14, BiocInstaller version 1.2.1. > Installing package(s) 'mirna20.db' > Installing package(s) into ?C:/Users/Peter > Davidsen/Documents/R/win-library/2.14? > (as ?lib? is unspecified) > Old packages: 'AnnotationDbi' > Update all/some/none? [a/s/n]: a > trying URL 'http://www.bioconductor.org/packages/2.9/bioc/bin/window s/contrib/2.14/AnnotationDbi_1.16.8.zip' > Content type 'application/zip' length 5667171 bytes (5.4 Mb) > opened URL > downloaded 5.4 Mb > > package ?AnnotationDbi? successfully unpacked and MD5 sums checked > > The downloaded packages are in > C:\Users\Peter > Davidsen\AppData\Local\Temp\RtmpWsjZYt\downloaded_packages > Warning messages: > 1: In getDependencies(pkgs, dependencies, available, lib) : > package ?mirna20.db? is not available (for R version 2.14.0) The package you want to install doesn't exist. I suppose it would be possible to create an annotation package for this chip, but not with the existing infrastructure. The miRNA2.0 chip has miRNA targets for 71 different species. In addition, each miRNA has on average 1000 different mRNA targets. So an annotation package would be really messy, and I am not sure it would be all that helpful. And think about what you would be asking with your nsfilter() call. A given miRNA can have around 1000 mRNA targets, and there are something like 1500 miRNAs for e.g., H. sapiens. Do you really want to eliminate all of them that have duplicate Entrez Gene IDs? In addition, miRNAs don't AFAIK have Entrez Gene IDs. But their targets do. So if you think about it, what you were trying to do isn't really a good idea. > 2: 'abind' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable That's a pretty clear error: it says that R doesn't have permission to write to the library directory. Windows > XP are all more Unix-like in that the permissions to do things have been seriously curtailed. You would have had to invoke administrator privileges to install R in that directory, and there may be problems installing things even if you run R as administrator. Anyway, I am not sure about the nitty-gritty details of getting R to install to the system library on newer versions of Windows, and frankly this isn't the place to ask. Your best bet is to go do a search on R-help (or google) for something like installed directory 'C:/Program Files/R/R-2.14.0/library' not writeable or some subset thereof. Best, Jim > 'acepack' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'AER' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'affy' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'affydata' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'affyio' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'affyPLM' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'affyQCReport' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'akima' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'annaffy' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0 [... truncated] > Any help would be appreciated > > > Many thanks, > Peter > > >> sessionInfo() > R version 2.14.0 (2011-10-31) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United > Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 > [4] LC_NUMERIC=C LC_TIME=English_United > Kingdom.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] genefilter_1.36.0 mirna20cdf_2.9.1 AnnotationDbi_1.16.8 > affy_1.32.0 Biobase_2.14.0 BiocInstaller_1.2.1 > > loaded via a namespace (and not attached): > [1] affyio_1.22.0 annotate_1.32.0 DBI_0.2-5 > IRanges_1.12.4 preprocessCore_1.16.0 RSQLite_0.10.0 > [7] splines_2.14.0 survival_2.36-10 tools_2.14.0 > xtable_1.6-0 zlibbioc_1.0.0 > > >> exprsFiltered<- nsFilter(exprs, remove.dupEntrez=F, var.cutoff=0.5)$eset > Error: getAnnMap: package mirna20 not available >> traceback() > 10: stop("getAnnMap: ", "package ", pkg, " not available", call. = FALSE) > 9: value[[3L]](cond) > 8: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > 7: tryCatchList(expr, classes, parentenv, handlers) > 6: tryCatch(as.environment(searchName), error = function(e) { > if (load) { > ok<- suppressWarnings(require(pkg, character.only = TRUE, > quietly = TRUE)) > if (!ok&& length(type)> 1) { > origPkg<- pkg > for (t in type[2:length(type)]) { > pkg<- annPkgName(name = chip, type = t) > searchName<- paste("package", pkg, sep = ":") > if (suppressWarnings(require(pkg, character.only = TRUE, > quietly = TRUE))) { > if (!typeMissed) > warning("getAnnMap: ", "package ", origPkg, > " not available, ", "using ", pkg, " instead", > call. = FALSE) > ok<- TRUE > break > } > } > } > if (!ok) > stop("getAnnMap: ", "package ", pkg, " not available", > call. = FALSE) > as.environment(searchName) > } > else { > stop("getAnnMap: ", pkg, " package not attached and load is FALSE", > call. = FALSE) > } > }) > 5: getAnnMap("_dbconn", chip) > 4: .findDBMeta(chip, "CENTRALID") > 3: .findCentralMap(annChip) > 2: nsFilter(exprs, remove.dupEntrez = F, var.cutoff = 0.5) > 1: nsFilter(exprs, remove.dupEntrez = F, var.cutoff = 0.5) > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > 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

Dear Peter if all you want to do is filter probesets with small variance, you may not need the complex 'nsFilter' function, and something as simple as x = ... your ExpressionSet ... rv = rowVars(exprs(x)) xfiltered = x[ rs > quantile(rv, probs=0.5), ] might do the job. Best wishes Wolfgang PS - the variable name 'exprs' is formally OK, but may look confusing since there is a useful function of the same name, and you will end up with expressions such as 'exprs(exprs)'. On 12/5/11 3:38 PM, Peter Davidsen wrote: > Dear List, > > I'm trying to filter some microRNA expression data generated on the > Affymetrix miRNA 2.0 array platform before running the DE genes > analysis. > However, I get an error when I apply the nsFilter function in the > genefilter package - see below: > > #### my script #### > #Set working dir > setwd("C:/Users/CEL") > > #produce a character vector of the names of the files > celfiles<- list.files(path="C:/Users/CEL") > > #load packages > library(affy) > library(mirna20cdf) > > #read CEL files and compute an expression measure > exprs<- justRMA(cdfname="mirna20", normalize=TRUE) #Create a > normalized exprSet object > > exprsFiltered<- nsFilter(exprs, remove.dupEntrez=F, var.cutoff=0.5)$eset > Error: getAnnMap: package mirna20 not available > > When I tried to install the "mirna20.db" annotation file: > >> source("http://bioconductor.org/biocLite.R") > BiocInstaller version 1.2.1, ?biocLite for help > >> biocLite("mirna20.db") > BioC_mirror: 'http://www.bioconductor.org' > Using R version 2.14, BiocInstaller version 1.2.1. > Installing package(s) 'mirna20.db' > Installing package(s) into ?C:/Users/Peter > Davidsen/Documents/R/win-library/2.14? > (as ?lib? is unspecified) > Old packages: 'AnnotationDbi' > Update all/some/none? [a/s/n]: a > trying URL 'http://www.bioconductor.org/packages/2.9/bioc/bin/window s/contrib/2.14/AnnotationDbi_1.16.8.zip' > Content type 'application/zip' length 5667171 bytes (5.4 Mb) > opened URL > downloaded 5.4 Mb > > package ?AnnotationDbi? successfully unpacked and MD5 sums checked > > The downloaded packages are in > C:\Users\Peter > Davidsen\AppData\Local\Temp\RtmpWsjZYt\downloaded_packages > Warning messages: > 1: In getDependencies(pkgs, dependencies, available, lib) : > package ?mirna20.db? is not available (for R version 2.14.0) > 2: 'abind' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'acepack' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'AER' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'affy' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'affydata' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'affyio' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'affyPLM' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'affyQCReport' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'akima' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0/library' not writeable > 'annaffy' cannot be updated, installed directory 'C:/Program > Files/R/R-2.14.0 [... truncated] >> > > Any help would be appreciated > > > Many thanks, > Peter > > >> sessionInfo() > R version 2.14.0 (2011-10-31) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United > Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 > [4] LC_NUMERIC=C LC_TIME=English_United > Kingdom.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] genefilter_1.36.0 mirna20cdf_2.9.1 AnnotationDbi_1.16.8 > affy_1.32.0 Biobase_2.14.0 BiocInstaller_1.2.1 > > loaded via a namespace (and not attached): > [1] affyio_1.22.0 annotate_1.32.0 DBI_0.2-5 > IRanges_1.12.4 preprocessCore_1.16.0 RSQLite_0.10.0 > [7] splines_2.14.0 survival_2.36-10 tools_2.14.0 > xtable_1.6-0 zlibbioc_1.0.0 > > >> exprsFiltered<- nsFilter(exprs, remove.dupEntrez=F, var.cutoff=0.5)$eset > Error: getAnnMap: package mirna20 not available >> traceback() > 10: stop("getAnnMap: ", "package ", pkg, " not available", call. = FALSE) > 9: value[[3L]](cond) > 8: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > 7: tryCatchList(expr, classes, parentenv, handlers) > 6: tryCatch(as.environment(searchName), error = function(e) { > if (load) { > ok<- suppressWarnings(require(pkg, character.only = TRUE, > quietly = TRUE)) > if (!ok&& length(type)> 1) { > origPkg<- pkg > for (t in type[2:length(type)]) { > pkg<- annPkgName(name = chip, type = t) > searchName<- paste("package", pkg, sep = ":") > if (suppressWarnings(require(pkg, character.only = TRUE, > quietly = TRUE))) { > if (!typeMissed) > warning("getAnnMap: ", "package ", origPkg, > " not available, ", "using ", pkg, " instead", > call. = FALSE) > ok<- TRUE > break > } > } > } > if (!ok) > stop("getAnnMap: ", "package ", pkg, " not available", > call. = FALSE) > as.environment(searchName) > } > else { > stop("getAnnMap: ", pkg, " package not attached and load is FALSE", > call. = FALSE) > } > }) > 5: getAnnMap("_dbconn", chip) > 4: .findDBMeta(chip, "CENTRALID") > 3: .findCentralMap(annChip) > 2: nsFilter(exprs, remove.dupEntrez = F, var.cutoff = 0.5) > 1: nsFilter(exprs, remove.dupEntrez = F, var.cutoff = 0.5) >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber