TCGAvisualize_starburst error for getMetPlatInfo() argument.

[NikolayAlabi]

Hello,

I have been having a huge struggle with the TCGAvisualize_starburst command.

starburst_lowvsint <- TCGAvisualize_starburst(met = acc.met.lowvsint, exp = dataDEGs_lowvsint, genome = "hg38", group1 = "low", group2 = "int", filename = "LowvsInt_starburst.png", met.platform = "450K", met.p.cut = 10^-5, exp.p.cut = 10^-5, diffmean.cut = 0.25, logFC.cut = 3, names = FALSE, height=10, width=15, dpi=300) Accessing grch37.ensembl.org to get gene information Downloading genome information (try:0) Using: Human genes (GRCh37.p13) o Fetching auxiliary information oo Fetching probes genomic information oo Fetching TSS information Downloading transcripts information. Using: Human genes (GRCh37.p13) o Mapping probes to nearest TSS o Mapping results information Error in [.data.frame(volcano, , diffcol) : undefined columns selected

Can anyone help me with this?

If you could please help me out on this as soon as possible. My TCGAbiolinks is updated to the most current version.

Best, Nikolay

R version 4.0.2 (2020-06-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/imkl/2018.3.222/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_gf_lp64.so

locale: [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8 [5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8 [7] LC_PAPER=en_CA.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] dplyr_1.0.1 SummarizedExperiment_1.18.2 [3] DelayedArray_0.14.1 matrixStats_0.56.0 [5] Biobase_2.48.0 GenomicRanges_1.40.0 [7] GenomeInfoDb_1.24.2 IRanges_2.22.2 [9] S4Vectors_0.26.1 sesameData_1.6.0 [11] ExperimentHub_1.14.2 AnnotationHub_2.20.2 [13] BiocFileCache_1.12.1 dbplyr_1.4.4 [15] BiocGenerics_0.34.0 TCGAbiolinks_2.16.4

loaded via a namespace (and not attached): [1] bitops_1.0-6 bit64_4.0.2 [3] RColorBrewer_1.1-2 progress_1.2.2 [5] httr_1.4.2 tools_4.0.2 [7] R6_2.4.1 HDF5Array_1.16.1 [9] DBI_1.1.0 colorspace_1.4-1 [11] DNAcopy_1.62.0 tidyselect_1.1.0 [13] prettyunits_1.1.1 preprocessCore_1.50.0 [15] bit_4.0.4 curl_4.3 [17] compiler_4.0.2 rvest_0.3.6 [19] xml2_1.3.2 scales_1.1.1 [21] randomForest_4.6-14 readr_1.3.1 [23] askpass_1.1 rappdirs_0.3.1 [25] stringr_1.4.0 digest_0.6.25 [27] R.utils_2.9.2 XVector_0.28.0 [29] pkgconfig_2.0.3 htmltools_0.5.0 [31] fastmap_1.0.1 rlang_0.4.7 [33] RSQLite_2.2.0 shiny_1.5.0 [35] generics_0.0.2 jsonlite_1.7.0 [37] wheatmap_0.1.0 BiocParallel_1.22.0 [39] R.oo_1.23.0 RCurl_1.98-1.2 [41] magrittr_1.5 GenomeInfoDbData_1.2.3 [43] Matrix_1.2-18 Rhdf5lib_1.10.1 [45] Rcpp_1.0.5 munsell_0.5.0 [47] lifecycle_0.2.0 R.methodsS3_1.8.0 [49] stringi_1.4.6 yaml_2.2.1 [51] zlibbioc_1.34.0 rhdf5_2.32.2 [53] plyr_1.8.6 grid_4.0.2 [55] blob_1.2.1 promises_1.1.1 [57] crayon_1.3.4 lattice_0.20-41 [59] hms_0.5.3 knitr_1.29 [61] pillar_1.4.6 biomaRt_2.44.4 [63] sesame_1.6.0 XML_3.99-0.5 [65] glue_1.4.1 BiocVersion_3.11.1 [67] downloader_0.4 data.table_1.13.0 [69] BiocManager_1.30.10 vctrs_0.3.2 [71] httpuv_1.5.4 gtable_0.3.0 [73] openssl_1.4.2 purrr_0.3.4 [75] tidyr_1.1.1 assertthat_0.2.1 [77] ggplot2_3.3.2 xfun_0.19 [79] mime_0.9 xtable_1.8-4 [81] later_1.1.0.1 tibble_3.0.3 [83] AnnotationDbi_1.50.3 memoise_1.1.0 [85] ellipsis_0.3.1 interactiveDisplayBase_1.26.3