[BioC] Error when using the nsFilter command in the genefilter package

[Peter Davidsen]

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)
>