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msk-mind / luna

Scripts for data processing
https://msk-mind.github.io/luna
Apache License 2.0
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About genomic_inventory_v1_FINAL.csv #391

Closed SZ-qing closed 1 year ago

SZ-qing commented 1 year ago

Hello, I'm using your code to prepare to reproduce the results of the article, and I see in the save_table_1A function on line 3586 of your lung_helpers.py file that it needs to read file ./omnibus/genomic_inventory_v1_FINAL.csv. May I ask where this you provide the

SZ-qing commented 1 year ago

In Figures-Finalized-Permutation-Test.ipynb ： df_clinical_old = pd.read_csv("/gpfs/mskmindhdp_emc/user/shared_data_folder/lung-mind-project/cohorts/MIND Cohort_v2_8August2020.csv") I don't see this file and other files included in this notebook, such as: lung_helpers.py--->line 407: df = pd.read_csv("/gpfs/mskmind_emc/data_user/aukermaa/LUNG_DATA/id_inventory_v3.csv")

armaank commented 1 year ago

Hi - some of those files aren't needed to the final analysis to reproduce results. Please refer to this synapse repository that contains the final data and code for the project: https://www.synapse.org/#!Synapse:syn26642505/wiki/615361

SZ-qing commented 1 year ago

In Figures-Finalized.ipynb to reproduct the Fig. 2D Fig. 3E Fig. 4C and Fig. 4D which need generate_auc_plot_V2 function. but this need results of get_null_mean_error function, which is producted by [https://github.com/msk-mind/luna/issues/391#issuecomment-1693026647]

armaank commented 1 year ago

Are you looking for access to the permuted data used for the permutation tests? If so, I can add them to the synapse repo.

SZ-qing commented 1 year ago

Yes, as above, I need it to repeat the result!

---- Replied Message ---- | From | @.> | | Date | 08/30/2023 21:25 | | To | @.> | | Cc | SZ-qing @.>, Author @.> | | Subject | Re: [msk-mind/luna] About genomic_inventory_v1_FINAL.csv (Issue #391) |

Are you looking for access to the permuted data used for the permutation tests? If so, I can add them to the synapse repo.

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armaank commented 1 year ago

Hi - I've updated the synapse page accordingly - please see the tests folder in the files section

SZ-qing commented 1 year ago

Thanks

---- Replied Message ---- | From | @.> | | Date | 08/30/2023 21:46 | | To | @.> | | Cc | SZ-qing @.>, Author @.> | | Subject | Re: [msk-mind/luna] About genomic_inventory_v1_FINAL.csv (Issue #391) |

Hi - I've updated the synapse page accordingly - please see the tests folder in the files section

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