Thanks for sharing this great package. I was trying to use liana to analyze my data, which was a SingleCellExperiment object that I have been using for a while.
When I tried to use liana_wrap directly, I found the following error:
Error in `map()`:
ℹ In index: 1.
ℹ With name: CellChatDB.
Caused by error in `map()`:
ℹ In index: 1.
Caused by error in `h()`:
! error in evaluating the argument 'x' in selecting a method for function 'calculateAverage': level sets of factors are different
Run `rlang::last_trace()` to see where the error occurred.
which wasn't really informative, using rlang::last_trace didn't revealed a lot either at first glance:
But it turned out that the reason that it was crashing was in the line S4Vectors::subset.Vector(sce, select = colLabels(sce) == subject) because I had a subject column in my colData. After changing the name of the column it worked fine, so I thought to let you know about this error because it can be easily addressed in the liana_prep function.
Hello,
Thanks for sharing this great package. I was trying to use liana to analyze my data, which was a
SingleCellExperiment
object that I have been using for a while.When I tried to use
liana_wrap
directly, I found the following error:which wasn't really informative, using rlang::last_trace didn't revealed a lot either at first glance:
But it turned out that the reason that it was crashing was in the line
S4Vectors::subset.Vector(sce, select = colLabels(sce) == subject)
because I had asubject
column in mycolData
. After changing the name of the column it worked fine, so I thought to let you know about this error because it can be easily addressed in theliana_prep
function.Thanks again, Rene