findReclassCells
Closed this issue · 4 comments
I am trying to use findReclassCells function, but getting the following error, even though the row names are unique.
reclass.cells <- findReclassCells(bar.table, names(final.calls)[which(final.calls=="Negative")])
[1] "Normalizing barode data..."
[1] "Pre-allocating data structures..."
Error in.rowNamesDF<-(x, value = value) :
duplicate 'row.names' are not allowed
In addition: Warning message:
non-unique values when setting 'row.names': ‘AAACCTGCAGCTCCGA-1’, ‘AAACGGGAGTGTACGG-1’, ‘AAACGGGCAATCAGAA-1’, ‘AAACGGGTCGACAGCC-1’, ‘AAAGCAACAAAGCAAT-1’, ‘AAATGCCGTTCAGTAC-1’, ‘AACACGTGTACTCTCC-1’, ‘AACACGTTCCGCATCT-1’, ‘AACCATGTCAGTGCAT-1’, ‘AACCATGTCCGTAGGC-1’
Hmmm, don't know what to say without a more information. Without meaning to sound too patronizing, my guess would be that your cellIDs included duplicates...
I got the same error and indeed some duplicates were introduced in the negative fraction. I didn't check at which step exactly but you can just filter them before running findReclassCells:
final.calls <- final.calls[!duplicated(names(final.calls))]
I was getting the same error as @sri540. Using the solution provided by @r-mvl, I was able to continue the analysis but now I am getting the following error:
[1] "Determining classifications for negative cells across all BCs, all q..."
Error in if (L == 0) warning("Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize'") :
missing value where TRUE/FALSE needed
Any idea of how to actually solve this?
hmmm... sort of hard to advise without the actual code. Could you forward along your code, as well as screenshots of what the data looks like (i.e., screenshot of head(cellIDs), head(bar.ref), head(bar.table), head(read.table), etc.)