I would like to analyze the data of multiple immunostaining images using the R package "phenoptr Reports "and "phenoptr".
I installed them according to the site below.
Several fanction were added to Addins.
However, when I ran "Consolidate and summarize" in Addine, I got the following error.
> phenoptrReports:::addin_20_consolidate()
要求されたパッケージ shiny をロード中です
Warning: パッケージ ‘shiny’ はバージョン 4.1.1 の R の下で造られました
Listening on http://127.0.0.1:6320
Reading "Merge_cell_seg_data".
Data is already in microns, no conversion performed
Warning: Error in split_phenotype_column: No positive phenotypes found.
3: shiny::runApp
2: shiny::runGadget
1: phenoptrReports:::addin_20_consolidate
I'm new to R and don't know the solution.
Could you please tell me what to do?
Today, I was finally able to resolve my error.
In my case, it was because I didn't put a "+" after the antigen name when making a list of Phenotypes in inForm Phenotyping.
"CD4+" or "CD8+"
"CD4" or "CD8"
Sometimes I merge with Inform, but sometimes I merge some ”Marge cell seg files” created from multiple projects with R.
For details, I found the following video, so please take a look if you like.