Hello,
My name is Shweta Johari and I am analysing my IHC data using phnoptr reports.
I have downloaded the R, R tools, r studio, phnoptr as mentioned by the akoya biosciences.
However, when I consolidate my merge data, only one project is getting consolidated and not the second.
I am receiving this message below and really don't know how to go ahead with this.
Can someone please help me?
phenoptrReports:::addin_20_consolidate()
Loading required package: shiny
Listening on http://127.0.0.1:7482
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!
My output is a consolidated txt file which cannot be used for the analysis and only one HTML file for mhc vim merged cell seg data.
May I please know how to go through this?
Thank you.
-Shweta Johari