Entering edit mode
Peter Davidsen
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210
@peter-davidsen-4584
Last seen 9.0 years ago
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)
>