mnnpy
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chriscainx
Cosine Normalization error
corrected = mnnpy.mnn_correct(D1, D4, var_subset=Gene_list, batch_categories =["Day1","Day4"])
Performing cosine normalization... multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/projects/academic/gbcstaff/utils/anaconda/lib/python3.6/multiprocessing/pool.py", line 119, in worker result = (True, func(*args, **kwds)) File "/projects/academic/gbcstaff/utils/anaconda/lib/python3.6/multiprocessing/pool.py", line 44, in mapstar return list(map(*args)) File "/projects/academic/gbcstaff/utils/anaconda/lib/python3.6/site-packages/numpy/linalg/linalg.py", line 2287, in norm return sqrt(add.reduce(s, axis=axis, keepdims=keepdims)) numpy.core._internal.AxisError: axis 1 is out of bounds for array of dimension 0 """
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "Preprocessing.py", line 65, in
Both D1 and D4 are anndata objects, Gene_list is a list of genes I would like to use
Looks like it's python's multiprocess problem, in the next version I will make a workaround
Hi Julien, could you update to 0.1.9.3 and check if the error occurs? Thank you!
Thanks for reaching out! I tried my same code this morning but a new error has been triggered.
Performing cosine normalization... multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "utils/anaconda/lib/python3.6/multiprocessing/pool.py", line 119, in worker result = (True, func(*args, **kwds)) File "utils/anaconda/lib/python3.6/multiprocessing/pool.py", line 44, in mapstar return list(map(*args)) File "utils/anaconda/lib/python3.6/site-packages/numpy/linalg/linalg.py", line 2287, in norm return sqrt(add.reduce(s, axis=axis, keepdims=keepdims)) numpy.core._internal.AxisError: axis 1 is out of bounds for array of dimension 0 """
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "Preprocessing.py", line 65, in
Let me know what you think! Julien
On Thu, May 24, 2018 at 4:40 AM, Chris Kang [email protected] wrote:
Hi Julien, could you update to 0.1.9.3 and check if the error occurs? Thank you!
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/chriscainx/mnnpy/issues/6#issuecomment-391636223, or mute the thread https://github.com/notifications/unsubscribe-auth/AQaKht9FKjwd7V3dicsaIMXHf-gpNXU_ks5t1nIAgaJpZM4T6SjI .
-- Julien Kann Bioinformatics Data Analyst UB Genomics and Bioinformatics Core
I may have figured out a work around.
I used this code instead: corrected = mnnpy.mnn_correct([D1, D4], var_subset=Gene_list, batch_categories =["Day1","Day4"])
adata = corrected[0]
print(D1) print(D4) print(adata)
The output of this is: AnnData object with n_obs × n_vars = 1930 × 33694 obs: 'n_counts' AnnData object with n_obs × n_vars = 1038 × 33694 obs: 'n_counts' [AnnData object with n_obs × n_vars = 1930 × 33694 obs: 'n_counts', AnnData object with n_obs × n_vars = 1038 × 33694 obs: 'n_counts']
Is this working as intended now?
On Thu, May 24, 2018 at 9:21 AM, Julien Kann [email protected] wrote:
Thanks for reaching out! I tried my same code this morning but a new error has been triggered.
Performing cosine normalization... multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "utils/anaconda/lib/python3.6/multiprocessing/pool.py", line 119, in worker result = (True, func(*args, **kwds)) File "utils/anaconda/lib/python3.6/multiprocessing/pool.py", line 44, in mapstar return list(map(*args)) File "utils/anaconda/lib/python3.6/site-packages/numpy/linalg/linalg.py", line 2287, in norm return sqrt(add.reduce(s, axis=axis, keepdims=keepdims)) numpy.core._internal.AxisError: axis 1 is out of bounds for array of dimension 0 """
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "Preprocessing.py", line 65, in
corrected = mnnpy.mnn_correct(D1, D4, var_subset=Gene_list, batch_categories =["Day1","Day4"]) File "utils/anaconda/lib/python3.6/site-packages/mnnpy/mnn.py", line 126, in mnn_correct svd_mode=svd_mode, do_concatenate=do_concatenate, **kwargs) File "utils/anaconda/lib/python3.6/site-packages/mnnpy/mnn.py", line 157, in mnn_correct var_subset, n_jobs) File "utils/anaconda/lib/python3.6/site-packages/mnnpy/utils.py", line 53, in transform_input_data in_scaling = p_n.map(l2_norm, in_batches) File "utils/anaconda/lib/python3.6/multiprocessing/pool.py", line 266, in map return self._map_async(func, iterable, mapstar, chunksize).get() File "utils/anaconda/lib/python3.6/multiprocessing/pool.py", line 644, in get raise self._value numpy.core._internal.AxisError: axis 1 is out of bounds for array of dimension 0 Let me know what you think! Julien
On Thu, May 24, 2018 at 4:40 AM, Chris Kang [email protected] wrote:
Hi Julien, could you update to 0.1.9.3 and check if the error occurs? Thank you!
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/chriscainx/mnnpy/issues/6#issuecomment-391636223, or mute the thread https://github.com/notifications/unsubscribe-auth/AQaKht9FKjwd7V3dicsaIMXHf-gpNXU_ks5t1nIAgaJpZM4T6SjI .
-- Julien Kann Bioinformatics Data Analyst UB Genomics and Bioinformatics Core
-- Julien Kann Bioinformatics Data Analyst UB Genomics and Bioinformatics Core
When I try to sc.pp.scale()
I get this result : AttributeError: 'list' object has no attribute 'mean'
On Thu, May 24, 2018 at 9:24 AM, Julien Kann [email protected] wrote:
I may have figured out a work around.
I used this code instead: corrected = mnnpy.mnn_correct([D1, D4], var_subset=Gene_list, batch_categories =["Day1","Day4"])
adata = corrected[0]
print(D1) print(D4) print(adata)
The output of this is: AnnData object with n_obs × n_vars = 1930 × 33694 obs: 'n_counts' AnnData object with n_obs × n_vars = 1038 × 33694 obs: 'n_counts' [AnnData object with n_obs × n_vars = 1930 × 33694 obs: 'n_counts', AnnData object with n_obs × n_vars = 1038 × 33694 obs: 'n_counts']
Is this working as intended now?
On Thu, May 24, 2018 at 9:21 AM, Julien Kann [email protected] wrote:
Thanks for reaching out! I tried my same code this morning but a new error has been triggered.
Performing cosine normalization... multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "utils/anaconda/lib/python3.6/multiprocessing/pool.py", line 119, in worker result = (True, func(*args, **kwds)) File "utils/anaconda/lib/python3.6/multiprocessing/pool.py", line 44, in mapstar return list(map(*args)) File "utils/anaconda/lib/python3.6/site-packages/numpy/linalg/linalg.py", line 2287, in norm return sqrt(add.reduce(s, axis=axis, keepdims=keepdims)) numpy.core._internal.AxisError: axis 1 is out of bounds for array of dimension 0 """
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "Preprocessing.py", line 65, in
corrected = mnnpy.mnn_correct(D1, D4, var_subset=Gene_list, batch_categories =["Day1","Day4"]) File "utils/anaconda/lib/python3.6/site-packages/mnnpy/mnn.py", line 126, in mnn_correct svd_mode=svd_mode, do_concatenate=do_concatenate, **kwargs) File "utils/anaconda/lib/python3.6/site-packages/mnnpy/mnn.py", line 157, in mnn_correct var_subset, n_jobs) File "utils/anaconda/lib/python3.6/site-packages/mnnpy/utils.py", line 53, in transform_input_data in_scaling = p_n.map(l2_norm, in_batches) File "utils/anaconda/lib/python3.6/multiprocessing/pool.py", line 266, in map return self._map_async(func, iterable, mapstar, chunksize).get() File "utils/anaconda/lib/python3.6/multiprocessing/pool.py", line 644, in get raise self._value numpy.core._internal.AxisError: axis 1 is out of bounds for array of dimension 0 Let me know what you think! Julien
On Thu, May 24, 2018 at 4:40 AM, Chris Kang [email protected] wrote:
Hi Julien, could you update to 0.1.9.3 and check if the error occurs? Thank you!
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/chriscainx/mnnpy/issues/6#issuecomment-391636223, or mute the thread https://github.com/notifications/unsubscribe-auth/AQaKht9FKjwd7V3dicsaIMXHf-gpNXU_ks5t1nIAgaJpZM4T6SjI .
-- Julien Kann Bioinformatics Data Analyst UB Genomics and Bioinformatics Core
-- Julien Kann Bioinformatics Data Analyst UB Genomics and Bioinformatics Core
-- Julien Kann Bioinformatics Data Analyst UB Genomics and Bioinformatics Core
Doesn't look right, could you add
mnnpy.settings.normalization='seq'
in the front (to circumvent python multiprocessing) and use the old code?
File "Preprocessing.py", line 65, in
On Thu, May 24, 2018 at 10:36 AM, Chris Kang [email protected] wrote:
Doesn't look right, could you add mnnpy.settings.normalization='seq' in the front (to circumvent python multiprocessing) and use the old code?
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/chriscainx/mnnpy/issues/6#issuecomment-391738046, or mute the thread https://github.com/notifications/unsubscribe-auth/AQaKhg2yBs8V_syMw8RnB6VEpJHx14zQks5t1sVWgaJpZM4T6SjI .
-- Julien Kann Bioinformatics Data Analyst UB Genomics and Bioinformatics Core