I am trying to get the SummarizedExperiment object from the TARGET-AML dataset with the following code:
`query <- GDCquery(project=c("TARGET-AML"),
data.category="Transcriptome Profiling",
data.type = "Gene Expression Quantification",
workflow.type = "STAR - Counts")
GDCdownload(query)
exp_data <- GDCprepare(query, summarizedExperiment = TRUE)`
But I get the following error:
Here is my sessionInfo:
`R version 4.5.0 (2025-04-11)
Platform: x86_64-pc-linux-gnu
Running under: AlmaLinux 9.7 (Moss Jungle Cat)
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.29.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=C.utf8 LC_NUMERIC=C LC_TIME=C.utf8 LC_COLLATE=C.utf8
[5] LC_MONETARY=C.utf8 LC_MESSAGES=C.utf8 LC_PAPER=C.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C.utf8 LC_IDENTIFICATION=C
time zone: UTC
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] remotes_2.5.0 dplyr_1.1.4 readxl_1.4.5 TCGAbiolinks_2.31.3
loaded via a namespace (and not attached):
[1] tidyselect_1.2.1 farver_2.1.2 blob_1.2.4
[4] filelock_1.0.3 Biostrings_2.76.0 S7_0.2.0
[7] fastmap_1.2.0 BiocFileCache_2.16.2 XML_3.99-0.19
[10] digest_0.6.37 lifecycle_1.0.4 KEGGREST_1.48.1
[13] RSQLite_2.4.3 magrittr_2.0.4 compiler_4.5.0
[16] rlang_1.1.6 progress_1.2.3 tools_4.5.0
[19] yaml_2.3.10 data.table_1.17.8 knitr_1.50
[22] prettyunits_1.2.0 S4Arrays_1.8.1 bit_4.6.0
[25] curl_7.0.0 DelayedArray_0.34.1 plyr_1.8.9
[28] xml2_1.4.1 RColorBrewer_1.1-3 abind_1.4-8
[31] withr_3.0.2 purrr_1.1.0 BiocGenerics_0.54.0
[34] grid_4.5.0 stats4_4.5.0 ggplot2_4.0.0
[37] scales_1.4.0 biomaRt_2.64.0 SummarizedExperiment_1.38.1
[40] cli_3.6.5 rmarkdown_2.30 crayon_1.5.3
[43] generics_0.1.4 tzdb_0.5.0 httr_1.4.7
[46] DBI_1.2.3 cachem_1.1.0 stringr_1.5.2
[49] rvest_1.0.5 TCGAbiolinksGUI.data_1.28.0 AnnotationDbi_1.70.0
[52] cellranger_1.1.0 XVector_0.48.0 matrixStats_1.5.0
[55] vctrs_0.6.5 Matrix_1.7-4 jsonlite_2.0.0
[58] IRanges_2.42.0 hms_1.1.4 S4Vectors_0.48.0
[61] bit64_4.6.0-1 tidyr_1.3.1 glue_1.8.0
[64] stringi_1.8.7 gtable_0.3.6 GenomeInfoDb_1.44.3
[67] GenomicRanges_1.60.0 UCSC.utils_1.4.0 tibble_3.3.0
[70] pillar_1.11.1 rappdirs_0.3.3 htmltools_0.5.8.1
[73] GenomeInfoDbData_1.2.14 R6_2.6.1 dbplyr_2.5.1
[76] httr2_1.2.1 evaluate_1.0.5 lattice_0.22-7
[79] Biobase_2.68.0 readr_2.1.5 png_0.1-8
[82] memoise_2.0.1 Rcpp_1.1.0 SparseArray_1.8.1
[85] downloader_0.4.1 xfun_0.53 MatrixGenerics_1.20.0
[88] pkgconfig_2.0.3`
Any help you could provide would be appreciated!
I am trying to get the SummarizedExperiment object from the TARGET-AML dataset with the following code:
`query <- GDCquery(project=c("TARGET-AML"),
data.category="Transcriptome Profiling",
data.type = "Gene Expression Quantification",
workflow.type = "STAR - Counts")
GDCdownload(query)
exp_data <- GDCprepare(query, summarizedExperiment = TRUE)`
But I get the following error:
Here is my sessionInfo:
`R version 4.5.0 (2025-04-11)
Platform: x86_64-pc-linux-gnu
Running under: AlmaLinux 9.7 (Moss Jungle Cat)
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.29.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=C.utf8 LC_NUMERIC=C LC_TIME=C.utf8 LC_COLLATE=C.utf8
[5] LC_MONETARY=C.utf8 LC_MESSAGES=C.utf8 LC_PAPER=C.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C.utf8 LC_IDENTIFICATION=C
time zone: UTC
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] remotes_2.5.0 dplyr_1.1.4 readxl_1.4.5 TCGAbiolinks_2.31.3
loaded via a namespace (and not attached):
[1] tidyselect_1.2.1 farver_2.1.2 blob_1.2.4
[4] filelock_1.0.3 Biostrings_2.76.0 S7_0.2.0
[7] fastmap_1.2.0 BiocFileCache_2.16.2 XML_3.99-0.19
[10] digest_0.6.37 lifecycle_1.0.4 KEGGREST_1.48.1
[13] RSQLite_2.4.3 magrittr_2.0.4 compiler_4.5.0
[16] rlang_1.1.6 progress_1.2.3 tools_4.5.0
[19] yaml_2.3.10 data.table_1.17.8 knitr_1.50
[22] prettyunits_1.2.0 S4Arrays_1.8.1 bit_4.6.0
[25] curl_7.0.0 DelayedArray_0.34.1 plyr_1.8.9
[28] xml2_1.4.1 RColorBrewer_1.1-3 abind_1.4-8
[31] withr_3.0.2 purrr_1.1.0 BiocGenerics_0.54.0
[34] grid_4.5.0 stats4_4.5.0 ggplot2_4.0.0
[37] scales_1.4.0 biomaRt_2.64.0 SummarizedExperiment_1.38.1
[40] cli_3.6.5 rmarkdown_2.30 crayon_1.5.3
[43] generics_0.1.4 tzdb_0.5.0 httr_1.4.7
[46] DBI_1.2.3 cachem_1.1.0 stringr_1.5.2
[49] rvest_1.0.5 TCGAbiolinksGUI.data_1.28.0 AnnotationDbi_1.70.0
[52] cellranger_1.1.0 XVector_0.48.0 matrixStats_1.5.0
[55] vctrs_0.6.5 Matrix_1.7-4 jsonlite_2.0.0
[58] IRanges_2.42.0 hms_1.1.4 S4Vectors_0.48.0
[61] bit64_4.6.0-1 tidyr_1.3.1 glue_1.8.0
[64] stringi_1.8.7 gtable_0.3.6 GenomeInfoDb_1.44.3
[67] GenomicRanges_1.60.0 UCSC.utils_1.4.0 tibble_3.3.0
[70] pillar_1.11.1 rappdirs_0.3.3 htmltools_0.5.8.1
[73] GenomeInfoDbData_1.2.14 R6_2.6.1 dbplyr_2.5.1
[76] httr2_1.2.1 evaluate_1.0.5 lattice_0.22-7
[79] Biobase_2.68.0 readr_2.1.5 png_0.1-8
[82] memoise_2.0.1 Rcpp_1.1.0 SparseArray_1.8.1
[85] downloader_0.4.1 xfun_0.53 MatrixGenerics_1.20.0
[88] pkgconfig_2.0.3`
Any help you could provide would be appreciated!