Re: [Bioc-devel] GSE62944, empty EH164 and EH165
Thank you for bringing this to our attention. The resources were created with a previous version of SummarizedExperiment that were not compatible with the current version. New resources have been added and are visible in both release 3.6 and devel 3.7. Please note the new EH_id's: > library(ExperimentHub) > hub <- ExperimentHub() snapshotDate(): 2017-10-30 > 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... EH1043 | RNA-Sequencing and clinical data for 9246 tumor samples from The... EH1044 | RNA-Sequencing and clinical data for 741 normal samples from The... > x = gse[["EH1043"]] > x class: SummarizedExperiment dim: 23368 9264 metadata(0): assays(1): CancerRaw rownames(23368): 1/2-SBSRNA4 A1BG ... ZZZ3 tAKR rowData names(0): colnames(9264): TCGA-G9-A9S0-01A-11R-A41O-07 TCGA-E1-5318-01A-01R-1470-07 ... TCGA-A7-A0DC-01A-11R-A00Z-07 TCGA-A5-A0VQ-01A-11R-A104-07 colData names(549): bcr_patient_uuid bcr_patient_barcode ... lymph_nodes_aortic_pos_total CancerType > dim(x) [1] 23368 9264 > x = gse[["EH1044"]] > x class: SummarizedExperiment dim: 23368 741 metadata(0): assays(1): NormalRaw rownames(23368): 1/2-SBSRNA4 A1BG ... ZZZ3 tAKR rowData names(0): colnames(741): TCGA-K4-A3WV-11A-21R-A22U-07 TCGA-49-6742-11A-01R-1858-07 ... TCGA-BH-A0H5-11A-62R-A115-07 TCGA-22-5489-11A-01R-1635-07 colData names(2): sample type > dim(x) [1] 23368 741 Cheers, Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Ludwig Geistlinger <ludwig.geistlin...@sph.cuny.edu> Sent: Thursday, December 14, 2017 3:01:56 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] GSE62944, empty EH164 and EH165 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] stats4parallel 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_1.14.0IRanges_2.12.0 [7] S4Vectors_0.16.0 GSE62944_1.6.0 [9] GEOquery_2.46.8Biobase_2.38.0 [11] ExperimentHub_1.4.0AnnotationHub_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
Re: [Bioc-devel] GSE62944, empty EH164 and EH165
Great! Thanks for resolving this so fast. Ludwig From: Shepherd, Lori <lori.sheph...@roswellpark.org> Sent: Friday, December 15, 2017 1:48 PM To: Ludwig Geistlinger; bioc-devel@r-project.org Subject: Re: GSE62944, empty EH164 and EH165 Thank you for bringing this to our attention. The resources were created with a previous version of SummarizedExperiment that were not compatible with the current version. New resources have been added and are visible in both release 3.6 and devel 3.7. Please note the new EH_id's: > library(ExperimentHub) > hub <- ExperimentHub() snapshotDate(): 2017-10-30 > 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... EH1043 | RNA-Sequencing and clinical data for 9246 tumor samples from The... EH1044 | RNA-Sequencing and clinical data for 741 normal samples from The... > x = gse[["EH1043"]] > x class: SummarizedExperiment dim: 23368 9264 metadata(0): assays(1): CancerRaw rownames(23368): 1/2-SBSRNA4 A1BG ... ZZZ3 tAKR rowData names(0): colnames(9264): TCGA-G9-A9S0-01A-11R-A41O-07 TCGA-E1-5318-01A-01R-1470-07 ... TCGA-A7-A0DC-01A-11R-A00Z-07 TCGA-A5-A0VQ-01A-11R-A104-07 colData names(549): bcr_patient_uuid bcr_patient_barcode ... lymph_nodes_aortic_pos_total CancerType > dim(x) [1] 23368 9264 > x = gse[["EH1044"]] > x class: SummarizedExperiment dim: 23368 741 metadata(0): assays(1): NormalRaw rownames(23368): 1/2-SBSRNA4 A1BG ... ZZZ3 tAKR rowData names(0): colnames(741): TCGA-K4-A3WV-11A-21R-A22U-07 TCGA-49-6742-11A-01R-1858-07 ... TCGA-BH-A0H5-11A-62R-A115-07 TCGA-22-5489-11A-01R-1635-07 colData names(2): sample type > dim(x) [1] 23368 741 Cheers, Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Ludwig Geistlinger <ludwig.geistlin...@sph.cuny.edu> Sent: Thursday, December 14, 2017 3:01:56 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] GSE62944, empty EH164 and EH165 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] stats4parallel 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_1.14.0IRanges_2.12.0 [7] S4Vectors_0.16.0 GSE62944_1.6.0 [9] GEOquery_2.46.8Biobase_2.38.0 [11] Expe
[Bioc-devel] GSE62944, empty EH164 and EH165
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] stats4parallel 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_1.14.0IRanges_2.12.0 [7] S4Vectors_0.16.0 GSE62944_1.6.0 [9] GEOquery_2.46.8Biobase_2.38.0 [11] ExperimentHub_1.4.0AnnotationHub_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_1.3.1dplyr_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_1.1.0magrittr_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
