Hey, I am new to Bioconductor but tried to follow the install instructions to get DEXSeq. It seems to be installing the latest version but as seen in the sessionInfo it shows an earlier version number. When trying to use it cannot find the functions for the pasilla dataset. For example there is no DEXSeqDataSetFromHTSeq but there is a DEXSeq::read.HTSeqCounts but it does not recognize the SampleTable... Could you please help me figuring out what is going wrong? Thanks, Attila -- output of sessionInfo(): > DEXSeqDataSetFromHTSeq Error: object 'DEXSeqDataSetFromHTSeq' not found > sessionInfo() R version 3.0.3 (2014-03-06) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] DEXSeq_1.8.0 edgeR_3.4.2 limma_3.18.13 [4] DESeq2_1.2.10 RcppArmadillo_0.4.300.0 Rcpp_0.11.1 [7] GenomicRanges_1.14.4 XVector_0.2.0 IRanges_1.20.7 [10] DESeq_1.14.0 lattice_0.20-29 locfit_1.5-9.1 [13] Biobase_2.22.0 BiocGenerics_0.8.0 BiocInstaller_1.12.1 loaded via a namespace (and not attached): [1] annotate_1.40.1 AnnotationDbi_1.24.0 biomaRt_2.18.0 Biostrings_2.30.1 [5] bitops_1.0-6 DBI_0.2-7 genefilter_1.44.0 geneplotter_1.40.0 [9] grid_3.0.3 hwriter_1.3 RColorBrewer_1.0-5 RCurl_1.95-4.1 [13] Rsamtools_1.14.3 RSQLite_0.11.4 splines_3.0.3 statmod_1.4.20 [17] stats4_3.0.3 stringr_0.6.2 survival_2.37-7 tools_3.0.3 [21] XML_3.95-0.2 xtable_1.7-3 zlibbioc_1.8.0 -- Sent via the guest posting facility at bioconductor.org.

On 03/06/14 00:07, Attila [guest] wrote: > It seems to be installing the latest version but as seen in the sessionInfo it shows an earlier version number. > R version 3.0.3 (2014-03-06) You need a current version of R (i.e., version 3.1) to get the current versions of Bioconductor packages. Simon