I am trying to apply diffxpy to my data which has about 300 cells on rows and about 17k genes on columns. I have two predefined clusters. When I try to run I get that error message. I have removed columns with all zero values from the matrix.
Error Message:
loading matrix: test_mat.txt
cl1
/mnt/ws/home/keynullazada/.conda/envs/p_env/lib/python3.7/site-packages/numpy/core/fromnumeric.py:3257: RuntimeWarning: Mean of empty slice.
out=out, **kwargs)
/mnt/ws/home/keynullazada/.conda/envs/p_env/lib/python3.7/site-packages/numpy/core/_methods.py:154: RuntimeWarning: invalid value encountered in true_divide
ret, rcount, out=ret, casting='unsafe', subok=False)
Traceback (most recent call last):
File "/mnt/dv/wid/projects5/Roy-singlecell/js_work/scripts/DEG_listing/diffxpy_ttest_DEG_listing.py", line 30, in
grouping="condition"
File "/mnt/dv/wid/projects5/Roy-singlecell/sridharanlab/data/perturb-seq/ke_work/scRNAseqalone_KE_custom/submatrices/diffxpy_DEG/batchglm/diffxpy/diffxpy/testing/tests.py", line 860, in t_test
is_sig_zerovar=is_sig_zerovar
File "/mnt/dv/wid/projects5/Roy-singlecell/sridharanlab/data/perturb-seq/ke_work/scRNAseqalone_KE_custom/submatrices/diffxpy_DEG/batchglm/diffxpy/diffxpy/testing/det.py", line 1572, in init
weights=np.array([x0.shape[0] / (x0.shape[0] + x1.shape[0]),
ZeroDivisionError: division by zero
Hi
I am trying to apply diffxpy to my data which has about 300 cells on rows and about 17k genes on columns. I have two predefined clusters. When I try to run I get that error message. I have removed columns with all zero values from the matrix.
Error Message:
looking forward to hearing from you
Khagani