Error in batch removal

[studyyan]

Hi,

Thank you for your excellent work with FlowCT.

My Mac is running R 4.3.3 version. I tried to use batch.removal() but I get the following error:

fcs_harmony <- batch.removal(fcs, method = "harmony", batch = "patient_id")
Initializing state using k-means centroids initialization
Harmony 1/10
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony 2/10
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony 3/10
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Harmony converged after 3 iterations
Error in assays<-(*tmp*, withDimnames = withDimnames, ..., value = *vtmp*) :
please use 'assay(x, withDimnames=FALSE)) <- value' or 'assays(x, withDimnames=FALSE)) <- value' when the rownames or colnames
of the supplied assay(s) are not identical to those of the receiving SingleCellExperiment object 'x'
In addition: Warning messages:
1: HarmonyMatrix is deprecated and will be removed in the future from the API in the future
2: Quick-TRANSfer stage steps exceeded maximum (= 6136650)
3: Quick-TRANSfer stage steps exceeded maximum (= 6136650)

Did you ever have such issue or do you know how to fix this?

Thank you

[studyyan]

Hi there,

I also have another question about the clustering.flow from PARC method. Does the "markers.to.use" option still work? Because the results are similar no matter the number or ranges of markers.to.use I choose?

Thank you.

[jgarces02]

Hi @studyyan, I'll need some time to check it since I'm working in a different institution, but I'll try to fix it asap.

[jfoedfjwofa]

Excuse me for cutting in.

I encountered the same error message when I conducted batch removal using Harmony, so I would appreciate it if you could share the solution if you find it.

Thank you so much.