Hi,
I'm trying to obtain the most recent version of GSE62944 from ExperimentHub via > library(ExperimentHub) > hub <- ExperimentHub() > gse <- AnnotationHub::query(hub, "GSE62944") > gse ExperimentHub with 3 records # snapshotDate(): 2017-10-30 # $dataprovider: GEO # $species: Homo sapiens # $rdataclass: SummarizedExperiment, ExpressionSet # additional mcols(): taxonomyid, genome, description, # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags, # rdatapath, sourceurl, sourcetype # retrieve records with, e.g., 'object[["EH1"]]' title EH1 | RNA-Sequencing and clinical data for 7706 tumor samples from The... EH164 | RNA-Sequencing and clinical data for 9246 tumor samples from The... EH165 | RNA-Sequencing and clinical data for 741 normal samples from The... Retrieving the original (outdated) dataset works fine: > x <- gse[["EH1"]] > dim(x) Features Samples 23368 7706 However, obtaining the most recent version of the data via > x <- gse[["EH164"]] gives me: > dim(x) NULL > class(x) [1] "SummarizedExperiment0" attr(,"package") [1] "SummarizedExperiment" > str(x) Formal class 'SummarizedExperiment0' [package "SummarizedExperiment"] with 0 slots Named list() It would be great if this could be updated. Thanks a lot, Ludwig -- Dr. Ludwig Geistlinger CUNY School of Public Health > sessionInfo() R version 3.4.2 (2017-09-28) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.1 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib 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] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] SummarizedExperiment_1.8.0 DelayedArray_0.4.1 [3] matrixStats_0.52.2 GenomicRanges_1.30.0 [5] GenomeInfoDb_1.14.0 IRanges_2.12.0 [7] S4Vectors_0.16.0 GSE62944_1.6.0 [9] GEOquery_2.46.8 Biobase_2.38.0 [11] ExperimentHub_1.4.0 AnnotationHub_2.10.1 [13] BiocGenerics_0.24.0 loaded via a namespace (and not attached): [1] Rcpp_0.12.14 XVector_0.18.0 [3] BiocInstaller_1.28.0 compiler_3.4.2 [5] bindr_0.1 zlibbioc_1.24.0 [7] bitops_1.0-6 tools_3.4.2 [9] digest_0.6.12 bit_1.1-12 [11] lattice_0.20-35 RSQLite_2.0 [13] memoise_1.1.0 tibble_1.3.4 [15] pkgconfig_2.0.1 rlang_0.1.4 [17] Matrix_1.2-12 shiny_1.0.5 [19] DBI_0.7 curl_3.0 [21] yaml_2.1.14 bindrcpp_0.2 [23] GenomeInfoDbData_0.99.1 xml2_1.1.1 [25] httr_1.3.1 dplyr_0.7.4 [27] hms_0.3 grid_3.4.2 [29] bit64_0.9-7 glue_1.2.0 [31] R6_2.2.2 AnnotationDbi_1.40.0 [33] limma_3.34.3 purrr_0.2.4 [35] tidyr_0.7.2 readr_1.1.1 [37] blob_1.1.0 magrittr_1.5 [39] htmltools_0.3.6 assertthat_0.2.0 [41] mime_0.5 interactiveDisplayBase_1.16.0 [43] xtable_1.8-2 httpuv_1.3.5 [45] RCurl_1.95-4.8 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel