GDCprepare of RNAseq counts produces error
Entering edit mode
lescano ▴ 10
Last seen 10 weeks ago

Hello everyone!

I have been using the TCGAbiolinks package for the last couple years to access RNAseq data for the TCGA-LAML project. Just very recently, I had noticed that I could no longer use GDCquery to retrieve counts quantified by HT-seq (although I had been able to do so for years), and was prompted to use "STAR - Counts" instead.

When I fixed my code to reflect this, I get this error:

RNA_query <- GDCquery ( project = "TCGA-LAML",
                         data.category = "Transcriptome Profiling",
                         data.type = "Gene Expression Quantification",
                        workflow.type = "STAR - Counts", 
                        experimental.strategy = "RNA-Seq")
RNA_counts <- GDCprepare(RNA_query, summarizedExperiment = FALSE)
|=====================================================================|100%                      Completed after 35 s 
Error in `vectbl_as_col_location()`:
! Can't subset columns past the end.
ℹ Locations 2, 3, and 4 don't exist.
ℹ There is only 1 column.
Run `rlang::last_error()` to see where the error occurred.
There were 50 or more warnings (use warnings() to see the first 50)

> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.2.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] forcats_0.5.1       stringr_1.4.0       dplyr_1.0.8         purrr_0.3.4        
 [5] readr_2.1.2         tidyr_1.2.0         tibble_3.1.6        ggplot2_3.3.5      
 [9] tidyverse_1.3.1     edgeR_3.36.0        limma_3.50.1        TCGAbiolinks_2.22.4

loaded via a namespace (and not attached):
  [1] colorspace_2.0-3            ggsignif_0.6.3              rjson_0.2.21               
  [4] ellipsis_0.3.2              XVector_0.34.0              fs_1.5.2                   
  [7] GenomicRanges_1.46.1        rstudioapi_0.13             ggpubr_0.4.0               
 [10] bit64_4.0.5                 lubridate_1.8.0             AnnotationDbi_1.56.2       
 [13] fansi_1.0.3                 xml2_1.3.3                  splines_4.1.2              
 [16] R.methodsS3_1.8.1           cachem_1.0.6                knitr_1.38                 
 [19] jsonlite_1.8.0              Rsamtools_2.10.0            broom_0.7.12               
 [22] km.ci_0.5-2                 dbplyr_2.1.1                png_0.1-7                  
 [25] R.oo_1.24.0                 compiler_4.1.2              httr_1.4.2                 
 [28] backports_1.4.1             assertthat_0.2.1            Matrix_1.4-1               
 [31] fastmap_1.1.0               lazyeval_0.2.2              cli_3.2.0                  
 [34] prettyunits_1.1.1           tools_4.1.2                 gtable_0.3.0               
 [37] glue_1.6.2                  GenomeInfoDbData_1.2.7      rappdirs_0.3.3             
 [40] Rcpp_1.0.8.3                carData_3.0-5               Biobase_2.54.0             
 [43] cellranger_1.1.0            vctrs_0.4.0                 Biostrings_2.62.0          
 [46] rtracklayer_1.54.0          xfun_0.30                   rvest_1.0.2                
 [49] lifecycle_1.0.1             restfulr_0.0.13             ensembldb_2.18.4           
 [52] rstatix_0.7.0               XML_3.99-0.9                zlibbioc_1.40.0            
 [55] zoo_1.8-9                   scales_1.1.1                hms_1.1.1                  
 [58] MatrixGenerics_1.6.0        ProtGenerics_1.26.0         parallel_4.1.2             
 [61] SummarizedExperiment_1.24.0 AnnotationFilter_1.18.0     yaml_2.3.5                 
 [64] curl_4.3.2                  memoise_2.0.1               gridExtra_2.3              
 [67] KMsurv_0.1-5                downloader_0.4              biomaRt_2.50.3             
 [70] stringi_1.7.6               RSQLite_2.2.11              S4Vectors_0.32.4           
 [73] BiocIO_1.4.0                GenomicFeatures_1.46.5      BiocGenerics_0.40.0        
 [76] filelock_1.0.2              BiocParallel_1.28.3         GenomeInfoDb_1.30.1        
 [79] rlang_1.0.2                 pkgconfig_2.0.3             matrixStats_0.61.0         
 [82] bitops_1.0-7                TCGAbiolinksGUI.data_1.14.0 lattice_0.20-45            
 [85] GenomicAlignments_1.30.0    bit_4.0.4                   tidyselect_1.1.2           
 [88] plyr_1.8.7                  magrittr_2.0.3              R6_2.5.1                   
 [91] IRanges_2.28.0              generics_0.1.2              DelayedArray_0.20.0        
 [94] DBI_1.1.2                   withr_2.5.0                 haven_2.4.3                
 [97] pillar_1.7.0                survival_3.3-1              KEGGREST_1.34.0            
[100] abind_1.4-5                 RCurl_1.98-1.6              modelr_0.1.8               
[103] crayon_1.5.1                car_3.0-12                  survMisc_0.5.5             
[106] utf8_1.2.2                  BiocFileCache_2.2.1         tzdb_0.3.0                 
[109] progress_1.2.2              readxl_1.4.0                locfit_1.5-9.5             
[112] grid_4.1.2                  data.table_1.14.2           blob_1.2.2                 
[115] reprex_2.0.1                digest_0.6.29               xtable_1.8-4               
[118] R.utils_2.11.0              stats4_4.1.2                munsell_0.5.0              
[121] survminer_0.4.9

Any insight on why this is happening and how I may approach fixing the issue would be greatly appreciated!

TCGAbiolinks • 901 views
Entering edit mode
Last seen 4 weeks ago
Miami, US

I am updating the package to work with the latest GDC version.

Could you try updating the package from GitHub with

BiocManager::install("BioinformaticsFMRP/") BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")

Entering edit mode

Thanks, it works now. At first I had some trouble after the initial download it, but after restarting R it seems to have fixed it. Thanks for your hard work!

Entering edit mode

DELETED: I provided some misleading info and dont want to waste anybody's time, will get back when I try some more things


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