Invalid UTF-8
1
0
Entering edit mode
@5de2f9c2
Last seen 4 months ago
India

Getting the following error in readNanoStringGeoMxSet(), Error in sub(re, "", x, perl = TRUE): input string 1 is invalid UTF-8 Traceback:

  1. readNanoStringGeoMxSet(dccFiles = dccfiles, pkcFiles = pkc, phenoDataFile = SampleAnnotationFile, . phenoDataSheet = "Template", phenoDataDccColName = "Sample_ID", . protocolDataColNames = c("aoi", "roi"), experimentDataColNames = c("panel"))
  2. readPKCFile(pkcFiles, default_pkc_vers = defaultPKCVersions)
  3. lapply(file, function(pkc_file) { . rjson::fromJSON(file = pkc_file) . })
  4. lapply(file, function(pkc_file) { . rjson::fromJSON(file = pkc_file) . })
  5. FUN(X[[i]], ...)
  6. rjson::fromJSON(file = pkc_file)
  7. trimws(json_str)
  8. mysub(paste0(whitespace, "+$"), mysub(paste0("^", whitespace, . "+"), x))
  9. sub(re, "", x, perl = TRUE)
  10. is.factor(x)
  11. mysub(paste0("^", whitespace, "+"), x)
  12. sub(re, "", x, perl = TRUE) Code should be placed in three backticks as shown below

My code is as follows : readNanoStringGeoMxSet(dccFiles = dccfiles, pkcFiles = pkc, phenoDataFile = SampleAnnotationFile, phenoDataSheet = 'Template', phenoDataDccColName = "Sample_ID", protocolDataColNames = c("aoi", "roi"), experimentDataColNames = c("panel"))

sessionInfo( ) R version 4.3.2 (2023-10-31) Platform: x86_64-conda-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /userdata/shakti/tools/mambaforge/envs/spatial_seq/lib/libopenblasp-r0.3.21.so; LAPACK version 3.9.0

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

time zone: Asia/Kolkata tzcode source: system (glibc)

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

other attached packages: [1] readxl_1.4.3 GSEABase_1.64.0
[3] graph_1.80.0 annotate_1.80.0
[5] XML_3.99-0.16.1 AnnotationDbi_1.64.1
[7] msigdb_1.10.0 ggalluvial_0.12.5
[9] SpatialExperiment_1.12.0 SingleCellExperiment_1.24.0 [11] SummarizedExperiment_1.32.0 GenomicRanges_1.54.1
[13] GenomeInfoDb_1.38.6 IRanges_2.36.0
[15] MatrixGenerics_1.14.0 matrixStats_1.2.0
[17] standR_1.6.0 lubridate_1.9.3
[19] forcats_1.0.0 stringr_1.5.1
[21] dplyr_1.1.4 purrr_1.0.2
[23] readr_2.1.5 tidyr_1.3.1
[25] tibble_3.2.1 tidyverse_2.0.0
[27] GeoMxWorkflows_1.8.0 GeomxTools_3.6.2
[29] NanoStringNCTools_1.10.0 ggplot2_3.4.4
[31] S4Vectors_0.40.2 Biobase_2.62.0
[33] BiocGenerics_0.48.1

loaded via a namespace (and not attached): [1] splines_4.3.2 pbdZMQ_0.3-11 bitops_1.0-7
[4] cellranger_1.1.0 polyclip_1.10-6 lifecycle_1.0.4
[7] globals_0.16.2 lattice_0.22-5 MASS_7.3-60.0.1
[10] magrittr_2.0.3 rmarkdown_2.25 yaml_2.3.8
[13] spam_2.10-0 askpass_1.2.0 sp_2.1-3
[16] reticulate_1.35.0 cowplot_1.1.3 DBI_1.2.2
[19] minqa_1.2.6 RColorBrewer_1.1-3 abind_1.4-5
[22] zlibbioc_1.48.0 EnvStats_2.8.1 Rtsne_0.17
[25] RCurl_1.98-1.14 tweenr_2.0.2 GenomeInfoDbData_1.2.11 [28] ggrepel_0.9.5 listenv_0.9.1 pheatmap_1.0.12
[31] BiocStyle_2.30.0 umap_0.2.10.0 RSpectra_0.16-1
[34] parallelly_1.37.0 codetools_0.2-19 DelayedArray_0.28.0
[37] ggforce_0.4.1 tidyselect_1.2.0 outliers_0.15
[40] farver_2.1.1 lme4_1.1-35.1 base64enc_0.1-3
[43] jsonlite_1.8.8 progressr_0.14.0 systemfonts_1.0.5
[46] tools_4.3.2 Rcpp_1.0.12 glue_1.7.0
[49] SparseArray_1.2.4 xfun_0.42 ggthemes_5.1.0
[52] IRdisplay_1.1 withr_3.0.0 numDeriv_2016.8-1.1
[55] BiocManager_1.30.22 fastmap_1.1.1 GGally_2.2.1
[58] boot_1.3-28.1 fansi_1.0.6 openssl_2.1.1
[61] digest_0.6.34 timechange_0.3.0 R6_2.5.1
[64] colorspace_2.1-0 RSQLite_2.3.5 utf8_1.2.4
[67] generics_0.1.3 data.table_1.15.0 httr_1.4.7
[70] htmlwidgets_1.6.4 S4Arrays_1.2.0 ggstats_0.5.1
[73] pkgconfig_2.0.3 gtable_0.3.4 blob_1.2.4
[76] XVector_0.42.0 htmltools_0.5.7 dotCall64_1.1-1
[79] SeuratObject_5.0.1 scales_1.3.0 png_0.1-8
[82] knitr_1.45 tzdb_0.4.0 reshape2_1.4.4
[85] rjson_0.2.21 uuid_1.2-0 nlme_3.1-164
[88] nloptr_2.0.3 repr_1.1.6 cachem_1.0.8
[91] parallel_4.3.2 vipor_0.4.7 pillar_1.9.0
[94] grid_4.3.2 vctrs_0.6.5 xtable_1.8-4
[97] beeswarm_0.4.0 evaluate_0.23 magick_2.8.3
[100] cli_3.6.2 compiler_4.3.2 rlang_1.1.3
[103] crayon_1.5.2 future.apply_1.11.1 plyr_1.8.9
[106] ggbeeswarm_0.7.2 ggiraph_0.8.8 stringi_1.8.3
[109] lmerTest_3.1-3 munsell_0.5.0 Biostrings_2.70.2
[112] Matrix_1.6-5 IRkernel_1.3.2 hms_1.1.3
[115] patchwork_1.2.0 bit64_4.0.5 future_1.33.1
[118] KEGGREST_1.42.0 memoise_2.0.1 bit_4.0.5
```

GeoMxWorkflows • 437 views
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0
Entering edit mode
@vincent-j-carey-jr-4
Last seen 8 weeks ago
United States

You have a nice detailed traceback there. One of the files in pkc has characters that are not valid UTF-8. If you are working interactively you can pick element 7 of the traceback and look at the text that is being processed. Some functions in the utf8 package may help you to diagnose and reformat the offending text.

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