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  • DESeq2 SummarizedExperiment0 Error

    Hey,

    So it's been a while since I used DESeq - I was trying to get DESeq2 working and I run into an error just attempting to run the example code from the vignette, running:

    directory <- system.file("extdata", package="pasilla", mustWork=TRUE)
    sampleFiles <- grep("treated",list.files(directory),value=TRUE)
    sampleCondition <- sub("(.*treated).*","\\1",sampleFiles)
    sampleTable <- data.frame(sampleName = sampleFiles,
    fileName = sampleFiles,
    condition = sampleCondition)
    ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable,
    directory = directory,
    design= ~ condition)
    Gives me the following error:

    Error in initialize(value, ...) :
    cannot use object of class “SummarizedExperiment0” in new(): class “DESeqDataSet” does not extend that class
    My session info:

    R version 3.2.2 (2015-08-14)
    Platform: x86_64-apple-darwin13.4.0 (64-bit)
    Running under: OS X 10.10.5 (Yosemite)

    locale:
    [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

    attached base packages:
    [1] parallel stats4 stats graphics grDevices utils datasets methods base

    other attached packages:
    [1] BiocInstaller_1.20.0 pasilla_0.10.0 DESeq2_1.10.0 RcppArmadillo_0.6.100.0.0 Rcpp_0.12.1 GenomicRanges_1.22.0 GenomeInfoDb_1.6.0 IRanges_2.4.0 S4Vectors_0.8.0
    [10] BiocGenerics_0.16.0

    loaded via a namespace (and not attached):
    [1] RColorBrewer_1.1-2 futile.logger_1.4.1 plyr_1.8.3 XVector_0.10.0 futile.options_1.0.0 tools_3.2.2 zlibbioc_1.16.0 rpart_4.1-10
    [9] digest_0.6.8 RSQLite_1.0.0 annotate_1.48.0 gtable_0.1.2 lattice_0.20-33 DBI_0.3.1 proto_0.3-10 gridExtra_2.0.0
    [17] genefilter_1.52.0 stringr_1.0.0 cluster_2.0.3 locfit_1.5-9.1 nnet_7.3-11 grid_3.2.2 Biobase_2.30.0 AnnotationDbi_1.32.0
    [25] XML_3.98-1.3 survival_2.38-3 BiocParallel_1.4.0 foreign_0.8-66 latticeExtra_0.6-26 Formula_1.2-1 geneplotter_1.48.0 ggplot2_1.0.1
    [33] reshape2_1.4.1 lambda.r_1.1.7 magrittr_1.5 scales_0.3.0 Hmisc_3.17-0 MASS_7.3-44 splines_3.2.2 SummarizedExperiment_1.0.0
    [41] xtable_1.7-4 colorspace_1.2-6 stringi_0.5-5 acepack_1.3-3.3 munsell_0.4.2

    Any advice? Thanks!

  • #2
    Try restarting R. I think if you updated to the latest Bioc libs you might need a fresh start to get it working.

    Comment


    • #3
      Damnit, yep that solved it, can't believe I hadn't tried that. Thanks!

      Comment

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