CPTAC-3 GDCprepare not working for Methylation Beta Values

[ollemonrasl]

Hello!

I would like to work with Methylation Beta Values from CPTAC-3. After downloading them, GDCprepare gives me the error below:

CODE:

query_met <- GDCquery(
          project = "CPTAC-3,
          data.category = "DNA Methylation",
          data.type = "Methylation Beta Value")
GDCdownload(query_met)
met <- GDCprepare(query_met)

ERROR:

oo Reading 1863 files
|100%                      Completed after 41 m 
oo Merging 1863 files
Error in readDNAmethylation(files = files, cases = cases, summarizedExperiment = summarizedExperiment,  : 
  all(unlist(x %>% map(function(y) { .... is not TRUE
Calls: sourceWithProgress ... met_download_function -> GDCprepare -> readDNAmethylation -> stopifnot
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted

Warnings:

Warning messages:
1: In y[, 1]$V1 == x[[1]][, 1]$V1 :
  longer object length is not a multiple of shorter object length

Any idea how to solve this?

Thank you very much!

L

[tiagochst]

Thank you for the bug.

There are 2 different versions of the EPIC array and each has a different number of probes which was causing the issue. I am testing the fix now. You can install the version with the fix as follows:

devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks",ref = "devel")

Message ID: @.***>

[ollemonrasl]

Hi, thank you!

First of all, thank you very much for the quick answer.

I tried with a small set of samples and it worked, however with all of them (n=1863) it still gives me the same error.

I'll leave here the sessionInfo() just in case.

R version 4.1.3 (2022-03-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8      
 [8] LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] sesameData_1.12.0           rmarkdown_2.25              ExperimentHub_2.2.1         AnnotationHub_3.2.2         BiocFileCache_2.2.1         dbplyr_2.4.0                data.table_1.14.8          
 [8] DT_0.30                     TCGAutils_1.14.1            stringr_1.5.1               dplyr_1.1.4                 SummarizedExperiment_1.24.0 Biobase_2.54.0              GenomicRanges_1.46.1       
[15] GenomeInfoDb_1.30.1         IRanges_2.28.0              S4Vectors_0.32.4            BiocGenerics_0.40.0         MatrixGenerics_1.6.0        matrixStats_1.1.0           TCGAbiolinks_2.29.6        

loaded via a namespace (and not attached):
 [1] colorspace_2.1-0              rjson_0.2.21                  ellipsis_0.3.2                XVector_0.34.0                rstudioapi_0.15.0             listenv_0.9.0                
 [7] MultiAssayExperiment_1.20.0   bit64_4.0.5                   interactiveDisplayBase_1.32.0 AnnotationDbi_1.56.2          fansi_1.0.5                   xml2_1.3.5                   
[13] codetools_0.2-19              cachem_1.0.8                  knitr_1.45                    jsonlite_1.8.7                Rsamtools_2.10.0              png_0.1-8                    
[19] shiny_1.7.5.1                 BiocManager_1.30.22           readr_2.1.4                   compiler_4.1.3                httr_1.4.7                    Matrix_1.6-3                 
[25] fastmap_1.1.1                 cli_3.6.1                     later_1.3.1                   htmltools_0.5.7               prettyunits_1.2.0             tools_4.1.3                  
[31] gtable_0.3.4                  glue_1.6.2                    GenomeInfoDbData_1.2.7        rappdirs_0.3.3                Rcpp_1.0.11                   vctrs_0.6.4                  
[37] Biostrings_2.62.0             rtracklayer_1.54.0            xfun_0.41                     globals_0.16.2                rvest_1.0.3                   mime_0.12                    
[43] lifecycle_1.0.4               restfulr_0.0.15               XML_3.99-0.15                 future_1.33.0                 zlibbioc_1.40.0               scales_1.2.1                 
[49] hms_1.1.3                     promises_1.2.1                parallel_4.1.3                yaml_2.3.7                    curl_5.1.0                    memoise_2.0.1                
[55] ggplot2_3.4.4                 downloader_0.4                biomaRt_2.50.3                stringi_1.8.1                 RSQLite_2.3.3                 BiocVersion_3.14.0           
[61] BiocIO_1.4.0                  GenomicDataCommons_1.18.0     GenomicFeatures_1.46.5        filelock_1.0.2                BiocParallel_1.28.3           rlang_1.1.1                  
[67] pkgconfig_2.0.3               bitops_1.0-7                  evaluate_0.23                 TCGAbiolinksGUI.data_1.15.1   lattice_0.22-5                purrr_1.0.2                  
[73] GenomicAlignments_1.30.0      htmlwidgets_1.6.2             bit_4.0.5                     tidyselect_1.2.0              parallelly_1.36.0             plyr_1.8.9                   
[79] magrittr_2.0.3                R6_2.5.1                      generics_0.1.3                DelayedArray_0.20.0           DBI_1.1.3                     pillar_1.9.0                 
[85] KEGGREST_1.34.0               RCurl_1.98-1.13               tibble_3.2.1                  crayon_1.5.2                  utf8_1.2.4                    tzdb_0.4.0                   
[91] progress_1.2.2                grid_4.1.3                    blob_1.2.4                    digest_0.6.33                 xtable_1.8-4                  tidyr_1.3.0                  
[97] httpuv_1.6.12                 munsell_0.5.0                 sessioninfo_1.2.2            

Am I missing something?

Thanks again! L

[LeaLe88]

Thank you for posting this. I am facing the same issue. Can anyone advise us on this?

Best Regards, Lea