Hello,
I am using the software phenoptr by akoya biosciences and when I run the merge data to consolidate the data, I am only getting one summary report of one project. Then it quits. Would you be able to assist me on this please?
However, I merged my data using inFORM but when I use the consolidated and summary in R addins. I only receive one summary report HTML of one project and not two. The two projects do not get consolidated or summarised.
I am receiving the following: phenoptrReports:::addin_20_consolidate() Loading required package: shiny
Listening on http://127.0.0.1:7199 Reading "merged_f4-80_sma_cd31_cell_seg_data". Data is already in microns, no conversion performed
Adding Slide ID column to merged_f4-80_sma_cd31_cell_seg_data.txt Writing report for "merged_f4-80_sma_cd31_cell_seg_data". Loading required package: UpSetR Quitting from lines 174-196 (Cell_seg_summary_report.Rmd) Unable to write summary report All renaming inputs must be named. Reading "mhc2 vim_cell_seg_data". Data is already in microns, no conversion performed
Adding Slide ID column to mhc2 vim_cell_seg_data.txt Writing report for "mhc2 vim_cell_seg_data". geom_path: Each group consists of only one observation. Do you need to adjust the group aesthetic? geom_path: Each group consists of only one observation. Do you need to adjust the group aesthetic? Writing consolidated data. Writing report for consolidated data.
Quitting from lines 174-196 (Cell_seg_summary_report.Rmd) Unable to write summary report All renaming inputs must be named. Done! >
Hello, I am using the software phenoptr by akoya biosciences and when I run the merge data to consolidate the data, I am only getting one summary report of one project. Then it quits. Would you be able to assist me on this please?
I have downloaded the phenoptr according to the installation instructions in the pdf link below: https://d1fgrgbaaj3jvk.cloudfront.net/wp-content/uploads/2020/05/PhenoptrRerports_Install_Instructions.v5.pdf
However, I merged my data using inFORM but when I use the consolidated and summary in R addins. I only receive one summary report HTML of one project and not two. The two projects do not get consolidated or summarised.
I am receiving the following: phenoptrReports:::addin_20_consolidate() Loading required package: shiny
Listening on http://127.0.0.1:7199 Reading "merged_f4-80_sma_cd31_cell_seg_data". Data is already in microns, no conversion performed Adding Slide ID column to merged_f4-80_sma_cd31_cell_seg_data.txt Writing report for "merged_f4-80_sma_cd31_cell_seg_data". Loading required package: UpSetR Quitting from lines 174-196 (Cell_seg_summary_report.Rmd) Unable to write summary report All renaming inputs must be named. Reading "mhc2 vim_cell_seg_data". Data is already in microns, no conversion performed Adding Slide ID column to mhc2 vim_cell_seg_data.txt Writing report for "mhc2 vim_cell_seg_data". geom_path: Each group consists of only one observation. Do you need to adjust the group aesthetic? geom_path: Each group consists of only one observation. Do you need to adjust the group aesthetic? Writing consolidated data. Writing report for consolidated data. Quitting from lines 174-196 (Cell_seg_summary_report.Rmd) Unable to write summary report All renaming inputs must be named. Done! >
Thank you for your help. Shweta Johari