[BioC] Problem with the oligo package for nimblegen analysis
isabelle goncalves [guest]
guest at bioconductor.org
Thu Oct 31 13:57:30 CET 2013
Hi,
I tried to reproduce the example of the MAQC study described in V2NExpression.pdf.
But, the command line
maqc <- read.xysfiles(xys.files, phenoData = pd)
gave the following output :
Platform design info loaded.
Checking designs for each XYS file... Done.
Allocating memory... Done.
Reading extdata/9868701_532.xys.
Reading extdata/9868901_532.xys.
Reading extdata/9869001_532.xys.
Reading extdata/9870301_532.xys.
Reading extdata/9870401_532.xys.
Reading extdata/9870601_532.xys.
Erreur dans validObject(out) : invalid class âExpressionFeatureSetâ object:
NChannelSet levels(varMetadata(object)$channel) / assayDataElementNames() mismatch; see ?"channelNames<-,NChannelSet,character-method"
traceback() gave :
> traceback()
3: stop(msg, ": ", errors, domain = NA)
2: validObject(out)
1: read.xysfiles(xys.files, phenoData = pd)
Any suggestions would be appreciated,
Thank you, Isabelle
-- output of sessionInfo():
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] pd.hg18.60mer.expr_3.4.0 RColorBrewer_1.0-5 limma_3.18.1 genefilter_1.44.0 maqcExpression4plex_1.6.3 pdInfoBuilder_1.26.0 oligo_1.26.0
[8] oligoClasses_1.24.0 affxparser_1.34.0 RSQLite_0.11.4 DBI_0.2-7 Biobase_2.22.0 BiocGenerics_0.8.0 BiocInstaller_1.12.0
loaded via a namespace (and not attached):
[1] affyio_1.30.0 annotate_1.40.0 AnnotationDbi_1.24.0 Biostrings_2.30.0 bit_1.1-10 codetools_0.2-8 ff_2.2-12 foreach_1.4.1
[9] GenomicRanges_1.14.3 IRanges_1.20.4 iterators_1.0.6 preprocessCore_1.24.0 splines_3.0.2 stats4_3.0.2 survival_2.37-4 tools_3.0.2
[17] XML_3.95-0.2 xtable_1.7-1 XVector_0.2.0 zlibbioc_1.8.0
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