DESeq2 SummarizedExperiment0 Error

[Beemo]

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!

[Michael Love]

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

[Beemo]

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