Error when using de.test.wald(): #227
Description
I am using diffxpy to calculate differential gene expression analysis, but every time the iteration for the calculation starts and is ended quickly with the same error. What could be the reason?
The code:
import diffxpy.api as de
Perform differential expression analysis
test_01 = de.test.wald(
data=adata_olig_2,
formula_loc="~ 1 + group",
factor_loc_totest="group",
gene_names=adata_olig.var_names,
sample_description=adata_olig.obs,
)
The error:
training location model: False
training scale model: True
iter 0: ll=56543949.613667
iter 1: ll=56543949.613667, converged: 0.00% (loc: 100.00%, scale update: False), in 0.00sec
Fitting 4000 dispersion models: (progress not available with multiprocessing)
BracketError: The algorithm terminated without finding a valid bracket. Consider trying different initial points.
Version information:
anndata 0.9.2
diffxpy v0.7.4
gseapy 1.0.6
numpy 1.24.4
pandas 1.5.3
scanpy 1.9.4
scipy 1.11.2