[BioC] Problem with the oligo package for nimblegen analysis

isabelle goncalves [guest] guest at bioconductor.org
Thu Oct 31 13:57:30 CET 2013


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 “ExpressionFeatureSet” 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)

[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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