Closed andreyurch closed 2 years ago
Hi Andrey,
Sorry for the slow response. There should be a few outputs from SignatureAnalyzer that would give you this information. All of this information can be found in the nmf_output.h5 file.
pd.read_hdf(<nmf_output.h5 path>, 'aggr')
pd.read_hdf(<nmf_output.h5 path> , 'W')
for fractional contributions and
pd.read_hdf(<nmf_output.h5 path>, 'Wraw')
for raw contributionspd.read_hdf(<nmf_output.h5 path>, 'H')
Hope this helps. Please let me know if you have any issues
Best regards, Yo
Dear developers,
I apologise for probably a simple question, but I was unable to find an answer in the Manual. I have a dataset of skin cancers and want: 1.Extract de novo signatures 2.Get optimal number of signatures for my dataset. 3.Get a table with the signatures of optimal number. 4.Get a table with exposure of signatures for each sample.
I run with the 96-chanell spectrum: signatureanalyzer -n 10 \ -t spectra \ --objective poisson \ --prior_on_H L1 \ --prior_on_W L1 \ 96_matrix_skin.txt
But how can I receive from output the optimal number of signatures, extracted signatures, exposures for my dataset?
Best regards, Andrey