garfield-hu
commented
5 months ago hi the same error occured to me today, is there any solution yet?
Open bhabakd opened 2 years ago
garfield-hu
commented
5 months ago hi the same error occured to me today, is there any solution yet?
Hi I have been trying to create a NGCHM object to visualize. I created the inferCNV object as suggested in their github page, using the infercnv::CreateInfercnvObject() followed by infercnv::run(). I am able to see the heatmap upon running infercnv::plot_cnv(). The 'ref_group_names' is set to my selected celltype.
However, upon running ngchm(infercnv_obj = tumor_CD3_infercnv_obj, out_dir = "C:/Users/bhaba/OneDrive/Documents/scRNAseq/infercnv/naive/CD3REF", path_to_shaidyMapGen = "C:/Users/bhaba/OneDrive/Documents/ShaidyMapGen.jar", gene_symbol = "bio.gene.hugo")
I encounter the following error: Error in tsvio::tsvGetData(file.path(blobdir, "matrix.tsv"), file.path(blobdir, : i/o or syntax error 9 processing indexfile 1
Regards
Bhabakd
FYI
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[1] C:/Users/bhaba/AppData/Local/R/win-library/4.2 [2] C:/Program Files/R/R-4.2.1/library
D ── DLL MD5 mismatch, broken installation.
─ Python configuration ──────────────────────────────────────────────────────────────────────────────────────────────── python: C:/Users/bhaba/AppData/Local/r-miniconda/envs/r-reticulate/python.exe libpython: C:/Users/bhaba/AppData/Local/r-miniconda/envs/r-reticulate/python38.dll pythonhome: C:/Users/bhaba/AppData/Local/r-miniconda/envs/r-reticulate version: 3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 05:59:00) [MSC v.1929 64 bit (AMD64)] Architecture: 64bit numpy: C:/Users/bhaba/AppData/Local/r-miniconda/envs/r-reticulate/Lib/site-packages/numpy numpy_version: 1.23.2 pandas: [NOT FOUND]
NOTE: Python version was forced by use_python function
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