Closed mHagiw closed 3 years ago
KevinMenden
commented
3 years ago Hi @mHagiw ,
sorry for the late response. This sounds indeed weird, I can't tell you right away how this happened. Did you figure it out by any chance, since you closed the issue?
mHagiw
commented
3 years ago Hi Kevin
I resolved my problem. I found inf in simulated data(.h5ad), not in bulk data.
So, I could run finally.
Thanks!!
Masaki Hagiwara
KevinMenden
commented
3 years ago Awesome, thanks for the explanation!
Hi,
Thanks for your great work on scaden.
I've been recently trying to use scaden to recognize cell fractions. With the newly released Scaden v1.1.2, I tried to run the 'scaden process' command but resulted in the same error showing
INFO Scaling using log_min_max functions.py:65 Traceback (most recent call last): File "/home/mhagiwara/Programs/anaconda3/envs/scaden/bin/scaden", line 8, in
sys.exit(main())
File "/home/mhagiwara/Programs/anaconda3/envs/scaden/lib/python3.9/site-packages/scaden/main.py", line 48, in main
cli()
File "/home/mhagiwara/Programs/anaconda3/envs/scaden/lib/python3.9/site-packages/click/core.py", line 1137, in call
return self.main(args, kwargs)
File "/home/mhagiwara/Programs/anaconda3/envs/scaden/lib/python3.9/site-packages/click/core.py", line 1062, in main
rv = self.invoke(ctx)
File "/home/mhagiwara/Programs/anaconda3/envs/scaden/lib/python3.9/site-packages/click/core.py", line 1668, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/mhagiwara/Programs/anaconda3/envs/scaden/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, ctx.params)
File "/home/mhagiwara/Programs/anaconda3/envs/scaden/lib/python3.9/site-packages/click/core.py", line 763, in invoke
return __callback(args, kwargs)
File "/home/mhagiwara/Programs/anaconda3/envs/scaden/lib/python3.9/site-packages/scaden/main.py", line 155, in process
processing(
File "/home/mhagiwara/Programs/anaconda3/envs/scaden/lib/python3.9/site-packages/scaden/process.py", line 35, in processing
preprocess_h5ad_data(raw_input_path=training_data,
File "/home/mhagiwara/Programs/anaconda3/envs/scaden/lib/python3.9/site-packages/scaden/model/functions.py", line 67, in preprocess_h5ad_data
raw_input.X = sample_scaling(raw_input.X, scaling_option)
File "/home/mhagiwara/Programs/anaconda3/envs/scaden/lib/python3.9/site-packages/scaden/model/functions.py", line 42, in sample_scaling
x = mms.fit_transform(x.T).T
File "/home/mhagiwara/Programs/anaconda3/envs/scaden/lib/python3.9/site-packages/sklearn/base.py", line 699, in fit_transform
return self.fit(X, fit_params).transform(X)
File "/home/mhagiwara/Programs/anaconda3/envs/scaden/lib/python3.9/site-packages/sklearn/preprocessing/_data.py", line 363, in fit
return self.partial_fit(X, y)
File "/home/mhagiwara/Programs/anaconda3/envs/scaden/lib/python3.9/site-packages/sklearn/preprocessing/_data.py", line 396, in partial_fit
X = self._validate_data(X, reset=first_pass,
File "/home/mhagiwara/Programs/anaconda3/envs/scaden/lib/python3.9/site-packages/sklearn/base.py", line 421, in _validate_data
X = check_array(X, *check_params)
File "/home/mhagiwara/Programs/anaconda3/envs/scaden/lib/python3.9/site-packages/sklearn/utils/validation.py", line 63, in inner_f
return f(args, kwargs)
File "/home/mhagiwara/Programs/anaconda3/envs/scaden/lib/python3.9/site-packages/sklearn/utils/validation.py", line 720, in check_array
_assert_all_finite(array,
File "/home/mhagiwara/Programs/anaconda3/envs/scaden/lib/python3.9/site-packages/sklearn/utils/validation.py", line 103, in _assert_all_finite
raise ValueError(
ValueError: Input contains infinity or a value too large for dtype('float32').**
My command for 'scaden process' is: scaden process tabula_MC38.h5ad dataset
I checked whether infinity data exist or not already.
We were successful when we changed only the genetic names. 2210010C04Rik (couldn't) ⇒ Foxp3 (OK!!)
May I have your suggestion on this issue? Thanks a lot!
Masaki