Entering edit mode
4.2 years ago
Rishabh Jha
•
0
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.
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.
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
No problem, Lord Rishabh