Comments (3)
And thanks for making this package !
Best regards,
Deniz Fettahoglu
from scgate.
Hello Deniz,
It looks like an issue with the SCT normalization, but it's hard to debug without seeing your code. Would you be able to provide a small example that reproduces these errors?
Best
-m
from scgate.
Hello,
I've solved the issue by precising the "assay" and the "reduction". I am using the data from Hao 2021 with the WNN pipeline. So there is always a need to precise which assay and which reduction to use.
Best,
Deniz Fettahoglu
from scgate.
Related Issues (20)
- new function to evaluate multiple models (list) with one command HOT 1
- new function to obtain a multi-class variable from a set of scGate models' pure/impure output HOT 3
- for merged datasets, allow for independent gating HOT 1
- Ucell scores for _additional_signatures_ not exported in multi-model mode [dev]
- plot_UCell_scores() fails unless scGate() is run with save.levels=T
- Use of pos.thr neg.thr HOT 2
- nn.idx with pre-calculated dimensionality reductions HOT 5
- Possible issue related to future / parallelism? HOT 1
- combining model_DBs HOT 6
- Add in custom scGATE db function
- Update models for blood cells HOT 1
- Create model for macrophages HOT 1
- kNN smoothing parameters HOT 1
- scGate as a multi-class classifier HOT 1
- Prepare for upcoming Seurat v5 release
- Discrepancy in genes included in block list between Human and Mouse
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