[Bioc-devel] GSE62944, empty EH164 and EH165
Ludwig Geistlinger
Ludwig.Geistlinger at sph.cuny.edu
Fri Dec 15 19:56:34 CET 2017
Great! Thanks for resolving this so fast. Ludwig
________________________________
From: Shepherd, Lori <Lori.Shepherd at RoswellPark.org>
Sent: Friday, December 15, 2017 1:48 PM
To: Ludwig Geistlinger; bioc-devel at 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-bounces at r-project.org> on behalf of Ludwig Geistlinger <Ludwig.Geistlinger at sph.cuny.edu>
Sent: Thursday, December 14, 2017 3:01:56 PM
To: bioc-devel at 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] 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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