Further clarification on cqc_fix() error message

[yls2g13]

Thanks for a great package. I was assuming the res$solution object provided would be able to find and rename old markers as it's in my res object. I'm getting an error message as below. I haven't found any examples that demonstrate how to work around this so writing here for more help.

Hope to hear from you!

error message

> cqc_fix(res)
Error in cf_rename_marker(x, from, to) : 
  old marker is not found: PE - TOX

code tried & output

library(flowCore)
library(flowWorkspace)
library(cytoqc)

> cqc_data <- cqc_load_fcs(files)
> check_results <- cqc_check(cqc_data, type = "marker")
> check_results
# A tibble: 3 × 3
  group_id  nFCS marker                                                                                                    
     <int> <int> <chr>                                                                                                     
1        2    22 CD44, CD45-1, CD62L, CD8, CX3CR1, CXCR5, Granzyme-B, Ki-67, L_D, PD-1, Slamf6, TCF-1, Tim-3, TOX          
2        1    20 A594 - TCF-1, APC - Granzyme-B, APCCy7 - CD62L, BUV395 - CD8, BUV737 - CD44, BV421 - Slamf6, BV605 - Tim-…
3        3    19 CD44, CD62L, CD8, CX3CR1, CXCR5, Granzyme-B, Ki-67, L_D, Ly5-1, PD-1, Slamf6, TCF-1, Tim-3, TOX           
> res <- cqc_match(check_results, ref = 2) 
Warning message:
Unmatched items remain after cqc_match. Before using cqc_fix, please resolve these unmatched items manually using cqc_match_update/remove/delete_unmatched or re-attempt automatic matching with cqc_match with a larger max.distance argument. 
> res <- cqc_match_delete_unmatched(res, c("PerCP-Cy5-5","Ly5-1"))
> cqc_fix(res)
Error in cf_rename_marker(x, from, to) : 
  old marker is not found: PE - TOX
> res
                    Ref                1     3
1                  CD44    BUV737 - CD44     ✓
2                CD45-1    FITC - CD45-1  <NA>
3                 CD62L   APCCy7 - CD62L     ✓
4                   CD8     BUV395 - CD8     ✓
5                CX3CR1   BV650 - CX3CR1     ✓
6                 CXCR5    PECy7 - CXCR5     ✓
7            Granzyme-B APC - Granzyme-B     ✓
8                 Ki-67             <NA>     ✓
9                   L_D       V500 - L_D     ✓
10                 PD-1     BV785 - PD-1     ✓
11               Slamf6   BV421 - Slamf6     ✓
12                TCF-1     A594 - TCF-1     ✓
13                Tim-3    BV605 - Tim-3     ✓
14                  TOX         PE - TOX     ✓
16 To Delete                 PerCP-Cy5-5 Ly5-1

> res$solution
# A tibble: 15 × 3
   group_id from             to        
      <int> <chr>            <chr>     
 1        1 PE - TOX         TOX       
 2        1 APC - Granzyme-B Granzyme-B
 3        1 A594 - TCF-1     TCF-1     
 4        1 FITC - CD45-1    CD45-1    
 5        1 V500 - L_D       L_D       
 6        1 BV421 - Slamf6   Slamf6    
 7        1 BV605 - Tim-3    Tim-3     
 8        1 BV650 - CX3CR1   CX3CR1    
 9        1 BV785 - PD-1     PD-1      
10        1 PECy7 - CXCR5    CXCR5     
11        1 APCCy7 - CD62L   CD62L     
12        1 BUV395 - CD8     CD8       
13        1 BUV737 - CD44    CD44      
14        1 PerCP-Cy5-5      NA        
15        3 Ly5-1            NA