On Thu, Jun 3, 2021 at 9:11 AM Shraddha Pai <shraddha.pai at utoronto.ca>
wrote:
Hi Vincent,
Thank you. This is for a workshop with pre-selected versions of R/BioC, so
I have no control over the release.
Will try redownloading the data. I just found it puzzling that the
identical code works in command-line R (ie started from bash shell) but not
in Rstudio but perhaps they have different ways of caching loaded MAE
objects?
Best,Shraddha
I neglected to mention that my transcript was developed in RStudio on
Terra, with RStudio 1.4.1106, 2389bc24
On Wed, Jun 2, 2021 at 4:28 PM Vincent Carey <stvjc at channing.harvard.edu>
wrote:
You are behind the release and should update. However, with a reasonably
close
instance I can't reproduce your error. I had a flaky download at one
point; you might
want to reconstitute your brca data.
brca = curatedTCGAData("BRCA", c("miRNASeqGene", "mRNAArray", "RPPAArray", "Methylation_methyl27"), dry.run=FALSE)snapshotDate(): 2020-10-27Working on: BRCA_miRNASeqGene-20160128see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentationdownloading 1 resourcesretrieving 1 resource |===================================================================================| 100%loading from cacheWorking on: BRCA_mRNAArray-20160128see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentationdownloading 1 resourcesretrieving 1 resource |===================================================================================| 100%loading from cacheWorking on: BRCA_RPPAArray-20160128see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentationdownloading 1 resourcesretrieving 1 resource |===================================================================================| 100%loading from cacheWorking on: BRCA_Methylation_methyl27-20160128see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentationloading from cachesee ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentationloading from cacheWorking on: BRCA_colData-20160128see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentationloading from cacheWorking on: BRCA_metadata-20160128see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentationloading from cacheWorking on: BRCA_sampleMap-20160128see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentationloading from cacheharmonizing input:
removing 11654 sampleMap rows not in names(experiments)
removing 1 colData rownames not in sampleMap 'primary'> brcaA MultiAssayExperiment object of 4 listed
experiments with user-defined names and respective classes.
Containing an ExperimentList class object of length 4:
[1] BRCA_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 849 columns
[2] BRCA_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 590 columns
[3] BRCA_RPPAArray-20160128: SummarizedExperiment with 226 rows and 937 columns
[4] BRCA_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 343 columns
Functionality:
experiments() - obtain the ExperimentList instance
colData() - the primary/phenotype DataFrame
sampleMap() - the sample coordination DataFrame
`$`, `[`, `[[` - extract colData columns, subset, or experiment
*Format() - convert into a long or wide DataFrame
assays() - convert ExperimentList to a SimpleList of matrices
exportClass() - save all data to files> assay(experiments(brca)[[4]])<27578 x 343> matrix of class DelayedMatrix and type "double":
TCGA-A1-A0SD-01A-11D-A112-05 ... TCGA-E2-A15T-01A-11D-A112-05
cg00000292 0.60555263 . 0.25951246
cg00002426 0.06197412 . 0.04144839
cg00003994 0.33345006 . 0.34969161
cg00005847 0.67217034 . 0.83666264
cg00006414 NA . NA
... . . .
cg27657283 0.04196141 . 0.03385843
cg27661264 0.51756951 . 0.47593756
cg27662379 0.01078112 . 0.01157093
cg27662877 0.03112835 . 0.02603354
cg27665659 0.01072116 . 0.01756740> sessionInfo()R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04 LTS
Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] rhdf5_2.34.0 curatedTCGAData_1.12.1 MultiAssayExperiment_1.16.0
[4] SummarizedExperiment_1.20.0 Biobase_2.50.0 GenomicRanges_1.42.0
[7] GenomeInfoDb_1.26.7 IRanges_2.24.1 S4Vectors_0.28.1
[10] BiocGenerics_0.36.1 MatrixGenerics_1.2.1 matrixStats_0.59.0
[13] httr_1.4.2 magrittr_2.0.1 AnVIL_1.5.0
[16] dplyr_1.0.6 BiocManager_1.30.15
loaded via a namespace (and not attached):
[1] bitops_1.0-7 bit64_4.0.5
[3] rprojroot_2.0.2 tools_4.0.3
[5] R6_2.5.0 HDF5Array_1.18.1
[7] DBI_1.1.1 colorspace_2.0-1
[9] rhdf5filters_1.2.1 withr_2.4.2
[11] tidyselect_1.1.1 prettyunits_1.1.1
[13] processx_3.5.2 bit_4.0.4
[15] curl_4.3.1 compiler_4.0.3
[17] cli_2.5.0 formatR_1.11
[19] DelayedArray_0.16.3 scales_1.1.1
[21] callr_3.7.0 rappdirs_0.3.3
[23] rapiclient_0.1.3 digest_0.6.27
[25] XVector_0.30.0 pkgconfig_2.0.3
[27] htmltools_0.5.1.1 dbplyr_2.1.1
[29] fastmap_1.1.0 rlang_0.4.11
[31] rstudioapi_0.13 RSQLite_2.2.7
[33] shiny_1.6.0 generics_0.1.0
[35] jsonlite_1.7.2 RCurl_1.98-1.3
[37] GenomeInfoDbData_1.2.4 futile.logger_1.4.3
[39] Matrix_1.3-2 Rcpp_1.0.6
[41] munsell_0.5.0 Rhdf5lib_1.12.1
[43] lifecycle_1.0.0 yaml_2.2.1
[45] zlibbioc_1.36.0 pkgbuild_1.2.0
[47] BiocFileCache_1.14.0 AnnotationHub_2.22.1
[49] grid_4.0.3 blob_1.2.1
[51] promises_1.2.0.1 ExperimentHub_1.16.1
[53] crayon_1.4.1 lattice_0.20-41
[55] ps_1.6.0 pillar_1.6.1
[57] futile.options_1.0.1 glue_1.4.2
[59] BiocVersion_3.12.0 lambda.r_1.2.4
[61] remotes_2.3.0 vctrs_0.3.8
[63] httpuv_1.6.1 gtable_0.3.0
[65] purrr_0.3.4 tidyr_1.1.3
[67] assertthat_0.2.1 cachem_1.0.5
[69] ggplot2_3.3.3 xfun_0.23
[71] mime_0.10 xtable_1.8-4
[73] later_1.2.0 tibble_3.1.2
[75] tinytex_0.32 AnnotationDbi_1.52.0
[77] memoise_2.0.0 ellipsis_0.3.2
[79] interactiveDisplayBase_1.28.0
On Wed, Jun 2, 2021 at 3:37 PM Shraddha Pai <shraddha.pai at utoronto.ca>
wrote:
Hello BioC community,
Calling assays() on a SummarizedExperiment object has suddenly started
giving me this error in Rstudio but not on command-line R. I have been
trying to solve this for a few hours without luck and any help would be
great. sessionInfo() output below and this is Rstudio 1.4.
Thanks,Shraddha
Browse[1]> brcaA MultiAssayExperiment object of 4 listed
experiments with user-defined names and respective classes.
Containing an ExperimentList class object of length 4:
[1] BRCA_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows
and 166 columns
[2] BRCA_mRNAArray-20160128: SummarizedExperiment with 17814 rows and
453 columns
[3] BRCA_RPPAArray-20160128: SummarizedExperiment with 226 rows and 362
columns
[4] BRCA_Methylation_methyl27-20160128: SummarizedExperiment with
27578 rows and 261 columns
Functionality:
experiments() - obtain the ExperimentList instance
colData() - the primary/phenotype DataFrame
sampleMap() - the sample coordination DataFrame
`$`, `[`, `[[` - extract colData columns, subset, or experiment
*Format() - convert into a long or wide DataFrame
assays() - convert ExperimentList to a SimpleList of matrices
exportClass() - save all data to files
Browse[1]> assays(experiments(brca)[[4]])Error in
.Call2("C_h5getdimscales", filepath, name, scalename, PACKAGE =
"HDF5Array") :
failed to open file '/root/.cache/ExperimentHub/661a6f10d826_2122'
Browse[2]> experiments(brca)[[4]]class: SummarizedExperiment
dim: 27578 261
metadata(0):
assays(1): counts
rownames(27578): cg00000292 cg00002426 ... cg27662877 cg27665659
rowData names(3): Gene_Symbol Chromosome Genomic_Coordinate
colnames(261): TCGA-A1-A0SD-01A-11D-A112-05 TCGA-A2-A04N-01A-11D-A112-05
...
TCGA-E2-A15S-01A-11D-A112-05 TCGA-E2-A15T-01A-11D-A112-05
colData names(0):
sessionInfo()R version 4.0.5 (2021-03-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS
Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/
libopenblasp-r0.3.8.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
LC_MESSAGES=C
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8
LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils
datasets methods
[9] base
other attached packages:
[1] rhdf5_2.34.0 netDx_1.2.3
[3] bigmemory_4.5.36 curatedTCGAData_1.12.1
[5] MultiAssayExperiment_1.16.0 SummarizedExperiment_1.20.0
[7] Biobase_2.50.0 GenomicRanges_1.42.0
[9] GenomeInfoDb_1.26.7 IRanges_2.24.1
[11] S4Vectors_0.28.1 BiocGenerics_0.36.1
[13] MatrixGenerics_1.2.1 matrixStats_0.58.0
loaded via a namespace (and not attached):
[1] uuid_0.1-4 AnnotationHub_2.22.1
[3] BiocFileCache_1.14.0 NMF_0.23.0
[5] plyr_1.8.6 igraph_1.2.6
[7] RCy3_2.10.2 lazyeval_0.2.2
[9] splines_4.0.5 entropy_1.3.0
[11] BiocParallel_1.24.1 scater_1.18.6
[13] rncl_0.8.4 ggplot2_3.3.3
[15] gridBase_0.4-7 digest_0.6.27
[17] foreach_1.5.1 htmltools_0.5.1.1
[19] viridis_0.6.1 fansi_0.4.2
[21] magrittr_2.0.1 memoise_2.0.0
[23] cluster_2.1.1 doParallel_1.0.16
[25] ROCR_1.0-11 limma_3.46.0
[27] annotate_1.68.0 R.utils_2.10.1
[29] prettyunits_1.1.1 colorspace_2.0-1
[31] blob_1.2.1 rappdirs_0.3.3
[33] xfun_0.23 dplyr_1.0.6
[35] crayon_1.4.1 RCurl_1.98-1.3
[37] bigmemory.sri_0.1.3 graph_1.68.0
[39] genefilter_1.72.1 phylobase_0.8.10
[41] survival_3.2-10 iterators_1.0.13
[43] ape_5.5 glue_1.4.2
[45] registry_0.5-1 gtable_0.3.0
[47] zlibbioc_1.36.0 XVector_0.30.0
[49] DelayedArray_0.16.3 BiocSingular_1.6.0
[51] kernlab_0.9-29 Rhdf5lib_1.12.1
[53] shape_1.4.6 SingleCellExperiment_1.12.0
[55] HDF5Array_1.18.1 scales_1.1.1
[57] DBI_1.1.1 edgeR_3.32.1
[59] rngtools_1.5 Rcpp_1.0.6
[61] viridisLite_0.4.0 xtable_1.8-4
[63] progress_1.2.2 rsvd_1.0.5
[65] bit_4.0.4 glmnet_4.1-1
[67] netSmooth_1.10.0 httr_1.4.2
[69] RColorBrewer_1.1-2 ellipsis_0.3.2
[71] scuttle_1.0.4 pkgconfig_2.0.3
[73] XML_3.99-0.6 R.methodsS3_1.8.1
[75] dbplyr_2.1.1 locfit_1.5-9.4
[77] utf8_1.2.1 RJSONIO_1.3-1.4
[79] howmany_0.3-1 tidyselect_1.1.1
[81] rlang_0.4.11 softImpute_1.4-1
[83] reshape2_1.4.4 later_1.2.0
[85] AnnotationDbi_1.52.0 munsell_0.5.0
[87] BiocVersion_3.12.0 tools_4.0.5
[89] cachem_1.0.5 generics_0.1.0
[91] RSQLite_2.2.7 ExperimentHub_1.16.1
[93] ade4_1.7-16 evaluate_0.14
[95] stringr_1.4.0 fastmap_1.1.0
[97] yaml_2.2.1 knitr_1.33
[99] bit64_4.0.5 purrr_0.3.4
[101] sparseMatrixStats_1.2.1 nlme_3.1-152
[103] mime_0.10 R.oo_1.24.0
[105] pracma_2.3.3 xml2_1.3.2
[107] compiler_4.0.5 beeswarm_0.3.1
[109] curl_4.3.1 interactiveDisplayBase_1.28.0
[111] tibble_3.1.2 RNeXML_2.4.5
[113] stringi_1.6.2 RSpectra_0.16-0
[115] lattice_0.20-41 Matrix_1.3-2
[117] vctrs_0.3.8 pillar_1.6.1
[119] lifecycle_1.0.0 rhdf5filters_1.2.1
[121] BiocManager_1.30.15 combinat_0.0-8
[123] BiocNeighbors_1.8.2 zinbwave_1.12.0
[125] data.table_1.14.0 irlba_2.3.3
[127] bitops_1.0-7 httpuv_1.6.1
[129] R6_2.5.0 promises_1.2.0.1
[131] gridExtra_2.3 vipor_0.4.5
[133] codetools_0.2-18 MASS_7.3-53.1
[135] assertthat_0.2.1 pkgmaker_0.32.2
[137] withr_2.4.2 GenomeInfoDbData_1.2.4
[139] locfdr_1.1-8 hms_1.1.0
[141] beachmat_2.6.4 grid_4.0.5
[143] tidyr_1.1.3 DelayedMatrixStats_1.12.3
[145] rmarkdown_2.8 Rtsne_0.15
[147] clusterExperiment_2.10.1 shiny_1.6.0
[149] ggbeeswarm_0.6.0 tinytex_0.31
--
*Shraddha Pai, PhD*
Principal Investigator
shraddhapai.com; @spaiglass on Twitter
*Ontario Institute for Cancer Research*
MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada
M5G
0A3
*@OICR_news* <https://twitter.com/oicr_news> | *www.oicr.on.ca*
<http://www.oicr.on.ca/>
*Collaborate. Translate. Change lives.*
This message and any attachments may contain confidentia...{{dropped:11}}