Not sure how to remedy this error
datadir <- file.path("~/Desktop/DSP DATA")
DCCFiles <- dir(file.path(datadir, "DCC"), pattern = ".dcc$", full.names = TRUE, recursive = TRUE)
PKCFiles <- dir(file.path(datadir, "PKC"), pattern = ".pkc$",full.names = TRUE, recursive = TRUE)
DCCFiles <- as.character(DCCFiles)
PKCFiles <- as.character(PKCFiles)
SampleAnnotationFile <- dir(file.path(datadir, "annotation"), pattern = ".xlsx$", full.names = TRUE, recursive = TRUE)
demoData <- readNanoStringGeoMxSet(dccFiles = DCCFiles, pkcFiles = PKCFiles, phenoDataFile = SampleAnnotationFile, phenoDataSheet = "Sheet1", phenoDataDccColName = "ROI_ID", protocolDataColNames = c("Segment Tag", "Scan Name"))
Output: Error: path
must be a string
please also include the results of running the following in an R session
sessionInfo( )
```R version 4.4.1 (2024-06-14) Platform: aarch64-apple-darwin20 Running under: macOS Monterey 12.6
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York tzcode source: internal
attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] GeoMxWorkflows_1.10.0 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4
[6] purrr_1.0.2 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 tidyverse_2.0.0
[11] BiocManager_1.30.23 GeomxTools_3.8.0 NanoStringNCTools_1.12.0 ggplot2_3.5.1 S4Vectors_0.42.1
[16] Biobase_2.64.0 BiocGenerics_0.50.0
loaded via a namespace (and not attached):
[1] readxl_1.4.3 rlang_1.1.4 magrittr_2.0.3 compiler_4.4.1 png_0.1-8
[6] systemfonts_1.1.0 vctrs_0.6.5 reshape2_1.4.4 pkgconfig_2.0.3 crayon_1.5.3
[11] fastmap_1.2.0 XVector_0.44.0 utf8_1.2.4 rmarkdown_2.27 tzdb_0.4.0
[16] UCSC.utils_1.0.0 nloptr_2.1.1 ggbeeswarm_0.7.2 xfun_0.46 zlibbioc_1.50.0
[21] GenomeInfoDb_1.40.1 jsonlite_1.8.8 EnvStats_2.8.1 tweenr_2.0.3 uuid_1.2-0
[26] parallel_4.4.1 R6_2.5.1 stringi_1.8.4 RColorBrewer_1.1-3 reticulate_1.38.0
[31] GGally_2.2.1 parallelly_1.37.1 boot_1.3-30 cellranger_1.1.0 numDeriv_2016.8-1.1
[36] knitr_1.48 Rcpp_1.0.13 future.apply_1.11.2 IRanges_2.38.1 igraph_2.0.3
[41] timechange_0.3.0 Matrix_1.7-0 splines_4.4.1 tidyselect_1.2.1 yaml_2.3.9
[46] rstudioapi_0.16.0 codetools_0.2-20 listenv_0.9.1 lattice_0.22-6 lmerTest_3.1-3
[51] plyr_1.8.9 withr_3.0.0 askpass_1.2.0 evaluate_0.24.0 Rtsne_0.17
[56] future_1.33.2 polyclip_1.10-7 ggstats_0.6.0 Biostrings_2.72.1 pillar_1.9.0
[61] generics_0.1.3 sp_2.1-4 hms_1.1.3 munsell_0.5.1 scales_1.3.0
[66] minqa_1.2.7 BiocStyle_2.32.1 globals_0.16.3 glue_1.7.0 pheatmap_1.0.12
[71] tools_4.4.1 data.table_1.15.4 lme4_1.1-35.5 RSpectra_0.16-2 ggiraph_0.8.10
[76] dotCall64_1.1-1 cowplot_1.1.3 grid_4.4.1 umap_0.2.10.0 colorspace_2.1-0
[81] networkD3_0.4 nlme_3.1-165 GenomeInfoDbData_1.2.12 ggforce_0.4.2 beeswarm_0.4.0
[86] vipor_0.4.7 cli_3.6.3 spam_2.10-0 fansi_1.0.6 ggthemes_5.1.0
[91] gtable_0.3.5 outliers_0.15 digest_0.6.36 progressr_0.14.0 ggrepel_0.9.5
[96] farver_2.1.2 rjson_0.2.21 htmlwidgets_1.6.4 SeuratObject_5.0.2 htmltools_0.5.8.1
[101] lifecycle_1.0.4 httr_1.4.7 openssl_2.2.0 MASS_7.3-61
What is the output from
traceback()
right after you get the error?Thanks for helping!
And this is the file path I get from print(sampleAnnotationFile)
[1] "/users/colinpierce/Desktop/DSP DATA/annotation/~$annotation.xlsx"
[2] "/users/colinpierce/Desktop/DSP DATA/annotation/annotation.xlsx"
In addition, I just tried to use an absolute path to the excel sheet
SampleAnnotationFile <- file.path("/users/colinpierce/Desktop/DSP DATA/annotation")
, and then I ran the same readNanoStringGeoMxSet line and got this output:Thanks again, I hope this helps