[Bioc-devel] GSE62944, empty EH164 and EH165

[Ludwig Geistlinger]

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Retrieving the original (outdated) dataset works fine: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


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