ValueError: Input contains infinity or a value too large for dtype('float32').

[mHagiw]

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

[KevinMenden]

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]

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]

Awesome, thanks for the explanation!