Question: ANALYZING DATA FROM GDC USING TCGAbiolinks.
0
gravatar for Rishabh Jha
7 months ago by
India
Rishabh Jha0 wrote:

Hello Everyone, I am a beginner in using TCGAbiolinks, lately, I have been using tutorials for the same from the official website. I wrote the same code as given on their website. Unfortunately, I got an error while preparing my data to Summarized Experiment using GDCprepare() function. The error says Error in fix.by(by.y, y): 'by' must specify a uniquely valid column - I tried to troubleshoot it using information available online, but the error still persists.

The Code that I applied is as given below:

install.packages("TCGAbiolinks")
install.packages("SummarizedExperiment")

library(TCGAbiolinks)
library(SummarizedExperiment)

devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks")

query <- GDCquery(project = "TCGA-GBM",
                  data.category = "Gene expression",
                  data.type = "Gene expression quantification",
                  platform = "Illumina HiSeq", 
                  file.type  = "normalized_results",
                  experimental.strategy = "RNA-Seq",
                  barcode = c("TCGA-14-0736-02A-01R-2005-01", "TCGA-06-0211-02A-02R-2005-01"),
                  legacy = TRUE)
GDCdownload(query, method = "api", files.per.chunk = 10)
data <- GDCprepare(query)

R Session Info:

R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 19.04

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.8.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.8.0

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

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

other attached packages:
 [1] TCGAbiolinks_2.15.3         SummarizedExperiment_1.12.0
 [3] DelayedArray_0.8.0          BiocParallel_1.16.6        
 [5] matrixStats_0.55.0          Biobase_2.42.0             
 [7] GenomicRanges_1.34.0        GenomeInfoDb_1.18.2        
 [9] IRanges_2.16.0              S4Vectors_0.20.1           
[11] BiocGenerics_0.28.0        

loaded via a namespace (and not attached):
  [1] backports_1.1.5               circlize_0.4.8               
  [3] AnnotationHub_2.14.5          aroma.light_3.12.0           
  [5] plyr_1.8.5                    selectr_0.4-2                
  [7] ConsensusClusterPlus_1.46.0   lazyeval_0.2.2               
  [9] splines_3.5.2                 usethis_1.5.1                
 [11] ggplot2_3.2.1                 sva_3.30.1                   
 [13] digest_0.6.25                 foreach_1.4.8                
 [15] htmltools_0.4.0               fansi_0.4.1                  
 [17] magrittr_1.5                  memoise_1.1.0                
 [19] cluster_2.0.7-1               doParallel_1.0.15            
 [21] remotes_2.1.1                 limma_3.38.3                 
 [23] ComplexHeatmap_1.20.0         Biostrings_2.50.2            
 [25] readr_1.3.1                   annotate_1.60.1              
 [27] sesameData_1.0.0              R.utils_2.9.2                
 [29] prettyunits_1.1.1             colorspace_1.4-1             
 [31] blob_1.2.1                    rvest_0.3.5                  
 [33] ggrepel_0.8.1                 xfun_0.12                    
 [35] dplyr_0.8.4                   callr_3.4.2                  
 [37] crayon_1.3.4                  RCurl_1.98-1.1               
 [39] jsonlite_1.6.1                genefilter_1.64.0            
 [41] zoo_1.8-7                     survival_3.1-8               
 [43] iterators_1.0.12              glue_1.3.1                   
 [45] survminer_0.4.6               gtable_0.3.0                 
 [47] sesame_1.0.0                  zlibbioc_1.28.0              
 [49] XVector_0.22.0                GetoptLong_0.1.8             
 [51] pkgbuild_1.0.6                wheatmap_0.1.0               
 [53] shape_1.4.4                   scales_1.1.0                 
 [55] DESeq_1.34.1                  DBI_1.1.0                    
 [57] edgeR_3.24.3                  ggthemes_4.2.0               
 [59] Rcpp_1.0.3                    xtable_1.8-4                 
 [61] progress_1.2.2                bit_1.1-15.2                 
 [63] matlab_1.0.2                  km.ci_0.5-2                  
 [65] preprocessCore_1.44.0         httr_1.4.1                   
 [67] RColorBrewer_1.1-2            ellipsis_0.3.0               
 [69] pkgconfig_2.0.3               XML_3.99-0.3                 
 [71] R.methodsS3_1.8.0             locfit_1.5-9.1               
 [73] DNAcopy_1.56.0                tidyselect_1.0.0             
 [75] rlang_0.4.4                   later_1.0.0                  
 [77] AnnotationDbi_1.44.0          munsell_0.5.0                
 [79] tools_3.5.2                   cli_2.0.1                    
 [81] downloader_0.4                generics_0.0.2               
 [83] RSQLite_2.2.0                 ExperimentHub_1.8.0          
 [85] devtools_2.2.2                broom_0.5.4                  
 [87] stringr_1.4.0                 fastmap_1.0.1                
 [89] yaml_2.2.1                    fs_1.3.1                     
 [91] processx_3.4.2                knitr_1.28                   
 [93] bit64_0.9-7                   survMisc_0.5.5               
 [95] purrr_0.3.3                   randomForest_4.6-14          
 [97] EDASeq_2.16.3                 nlme_3.1-137                 
 [99] mime_0.9                      R.oo_1.23.0                  
[101] xml2_1.2.2                    biomaRt_2.38.0               
[103] compiler_3.5.2                rstudioapi_0.11              
[105] curl_4.3                      interactiveDisplayBase_1.20.0
[107] testthat_2.3.1                ggsignif_0.6.0               
[109] tibble_2.1.3                  geneplotter_1.60.0           
[111] stringi_1.4.6                 ps_1.3.2                     
[113] desc_1.2.0                    GenomicFeatures_1.34.8       
[115] lattice_0.20-38               Matrix_1.2-15                
[117] KMsurv_0.1-5                  vctrs_0.2.3                  
[119] pillar_1.4.3                  lifecycle_0.1.0              
[121] BiocManager_1.30.10           GlobalOptions_0.1.1          
[123] data.table_1.12.8             bitops_1.0-6                 
[125] httpuv_1.5.2                  rtracklayer_1.42.2           
[127] R6_2.4.1                      latticeExtra_0.6-28          
[129] hwriter_1.3.2                 promises_1.1.0               
[131] ShortRead_1.40.0              gridExtra_2.3                
[133] sessioninfo_1.1.1             codetools_0.2-16             
[135] pkgload_1.0.2                 assertthat_0.2.1             
[137] rprojroot_1.3-2               rjson_0.2.20                 
[139] withr_2.1.2                   GenomicAlignments_1.18.1     
[141] Rsamtools_1.34.1              GenomeInfoDbData_1.2.0       
[143] mgcv_1.8-27                   hms_0.5.3                    
[145] grid_3.5.2                    tidyr_1.0.2                  
[147] ggpubr_0.2.5                  shiny_1.4.0

If anyone had encountered the same issue previously, kindly help.

rna-seq • 160 views
ADD COMMENTlink written 7 months ago by Rishabh Jha0

Which solutions have you tried? - have you come across these?

TCGAbiolinks is a comprehensive package and it's usually difficult for anybody who is NOT one of the developers to respond to these questions - as such, expectedly, these questions usually go unanswered.

You should post issues on the GitHub page, but link back here, now that you have already posted here.

ADD REPLYlink written 7 months ago by Kevin Blighe65k

Hello Sir, Yes, I had tried those solutions earlier. It was just that, I hadn't restarted my R session after updating TCGAbioliks. Thank you so much for replying to my query. I wouldn't have gone through the solution again if you hadn't replied. The error is now resolved.

Thank you so much, Sir

ADD REPLYlink modified 7 months ago • written 7 months ago by Rishabh Jha0

No problem, Lord Rishabh

ADD REPLYlink written 7 months ago by Kevin Blighe65k
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