[BioC] Error when using the nsFilter command in the genefilter package
Wolfgang Huber
whuber at embl.de
Mon Dec 5 22:46:43 CET 2011
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/windows/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)
>>
>
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--
Best wishes
Wolfgang
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber
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