GDCprepare error: all assays must have the same nrow and ncol

[gbrsales]

I'm using the following code to retrieve the gene expression data for TCGA-LUAD.

query <- GDCquery(
    project = "TCGA-LUAD",
    data.category = "Gene expression",
    data.type = "Gene expression quantification",
    platform = "Illumina HiSeq",
    experimental.strategy = "RNA-Seq",
    sample.type = "Primary Tumor",
    file.type = "results",
    legacy = TRUE)

GDCdownload(query, method = "api")
GDCprepare(query)

GDCprepare fails with the following error:

Error in method(object) : all assays must have the same nrow and ncol

If I now set file.type = "normalized_results" the download / preparation procedure completes successfully.

Here is a traceback of the failing code path:

12. stop("all assays must have the same nrow and ncol")
11. method(object)
10. validityMethod(as(object, superClass))
9. isTRUE(x)
8. anyStrings(validityMethod(as(object, superClass)))
7. validObject(assays)
6. Assays(assays, as.null.if.zero.assay = TRUE)
5. .new_RangedSummarizedExperiment(assays, rowRanges, colData, metadata)
4. SummarizedExperiment(assays = assays, rowRanges = rowRanges, colData = colData)
3. makeSEfromGeneExpressionQuantification(df, assay.list, genome = genome)
2. readGeneExpressionQuantification(files = files, cases = cases, 
summarizedExperiment = summarizedExperiment, genome = ifelse(query$legacy, 
"hg19", "hg38"), experimental.strategy = unique(query$results[[1]]$experimental_strategy))
1. GDCprepare(query)

[tiagochst]

Hi, please which TCGAbiolinks and SummarizedExperiment version do you have installed ?

I was able to run the first code on my side.

[gbrsales]

Hi, here is my sessionInfo.

R version 4.1.1 (2021-08-10)
Platform: x86_64-apple-darwin20.4.0 (64-bit)
Running under: macOS Big Sur 11.6

Matrix products: default
LAPACK: /usr/local/Cellar/r/4.1.1/lib/R/lib/libRlapack.dylib

locale:
[1] it_IT.UTF-8/it_IT.UTF-8/it_IT.UTF-8/C/it_IT.UTF-8/it_IT.UTF-8

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

other attached packages:
[1] TCGAbiolinks_2.21.8

loaded via a namespace (and not attached):
 [1] MatrixGenerics_1.4.3        Biobase_2.52.0              httr_1.4.2                 
 [4] tidyr_1.1.4                 bit64_4.0.5                 jsonlite_1.7.2             
 [7] R.utils_2.11.0              assertthat_0.2.1            stats4_4.1.1               
[10] BiocFileCache_2.0.0         blob_1.2.2                  GenomeInfoDbData_1.2.6     
[13] progress_1.2.2              pillar_1.6.3                RSQLite_2.2.8              
[16] lattice_0.20-45             glue_1.4.2                  downloader_0.4             
[19] digest_0.6.28               GenomicRanges_1.44.0        XVector_0.32.0             
[22] rvest_1.0.1                 colorspace_2.0-2            plyr_1.8.6                 
[25] Matrix_1.3-4                R.oo_1.24.0                 XML_3.99-0.8               
[28] pkgconfig_2.0.3             biomaRt_2.48.3              zlibbioc_1.38.0            
[31] purrr_0.3.4                 scales_1.1.1                tzdb_0.1.2                 
[34] tibble_3.1.5                KEGGREST_1.32.0             generics_0.1.0             
[37] TCGAbiolinksGUI.data_1.12.0 IRanges_2.26.0              ggplot2_3.3.5              
[40] ellipsis_0.3.2              cachem_1.0.6                SummarizedExperiment_1.22.0
[43] BiocGenerics_0.38.0         magrittr_2.0.1              crayon_1.4.1               
[46] memoise_2.0.0               R.methodsS3_1.8.1           fansi_0.5.0                
[49] xml2_1.3.2                  tools_4.1.1                 data.table_1.14.2          
[52] prettyunits_1.1.1           hms_1.1.1                   lifecycle_1.0.1            
[55] matrixStats_0.61.0          stringr_1.4.0               S4Vectors_0.30.2           
[58] munsell_0.5.0               DelayedArray_0.18.0         AnnotationDbi_1.54.1       
[61] Biostrings_2.60.2           compiler_4.1.1              GenomeInfoDb_1.28.4        
[64] rlang_0.4.11                grid_4.1.1                  RCurl_1.98-1.5             
[67] rstudioapi_0.13             rappdirs_0.3.3              bitops_1.0-7               
[70] gtable_0.3.0                DBI_1.1.1                   curl_4.3.2                 
[73] R6_2.5.1                    knitr_1.36                  dplyr_1.0.7                
[76] fastmap_1.1.0               bit_4.0.4                   utf8_1.2.2                 
[79] filelock_1.0.2              readr_2.0.2                 stringi_1.7.5              
[82] parallel_4.1.1              Rcpp_1.0.7                  vctrs_0.3.8                
[85] png_0.1-7                   dbplyr_2.1.1                tidyselect_1.1.1           
[88] xfun_0.26

[tiagochst]

@gbrsales Please, could you check if the last update fixed your problem?

[DarkHe007]

Im having the exact same issue, I've tried updating the package but it doesn't run.

[gbrsales]

@tiagochst Works for me, thanks!

[tiagochst]

@DarkHe007 Please install the github version BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")

[DarkHe007]

@tiagochst Thank you very much! That did the trick!