fazeliniah

I am using Philosopher version 4.1.0

I just tried the v.4.1.1 and got the same issue.

Hi Fengchao and team, Hope you all had a wonderful holiday. I am just wondering if there is an update for this issue. Thanks

Hi Fengchao, I tested the MSFragger 3.4 and 3.5 and they both work nicely with our HLA peptidome project. The issue was related to our RNA-derived fasta database. The presence...

Thank you so much your help and very useful tutorial. I have couple of questions and greatly appreciate your help. 1- It seems that the GlycoSearch does much better/faster when...

I generated the focused database but unfortunately (as you suggested) the Glycosearch failed with "a Runtime Error: "Run failed, Exception: Index was outside the bounds of the array". I used...

R version 4.2.1 (2022-06-23 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 14393) Matrix products: default locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252...

So sorry for the mishap. I am using 1.6.4. Here is the new sessioninfo. > sessionInfo() R version 4.2.1 (2022-06-23 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build...

I am using a very generic command for PathfindR. It works smoothly with older version of R. Here is the script: genes_of_interest_pathfindr %dplyr::filter(adj.P.Val < 0.05 ,abs(logFC) > 0.5) %>% dplyr::select(Gene,logFC,adj.P.Val)...

> run_pathfindR(genes_of_interest_pathfindr, plot_enrichment_chart = FALSE) `n_processes` is set to `iterations` because `iterations` < `n_processes` There is already a directory named "pathfindR_Results". Writing the result to "pathfindR_Results(9)" not to overwrite any...