Repeatability

[Counts-Xin]

sorry to bother you, I get different results with same code in different runs, that is I cannoot get the repeatable results, especially without marker genes information.

[nukappa]

Do you use the same number of cells and genes every time? If yes, the results should be reproducible. If you change any parameters like number of cells, number of locations, number of genes used, geometry etc., the reconstructions would be of course different.

[mjang2000]

I have also not been able to repeatable results. Every time I run the tutorial notebook, I get the same results as my previous runs, but the results are not the same as the results in the tutorial notebook. I realized that the files are not named exactly the same, so I substituted missing files for the closest file (i.e. "high_var_genes.txt" instead of "hvg.txt" for the "reconstruct_drosophila_embryo_tutorial.ipynb" notebook), but other than that, I have not changed anything. I was wondering why this may be the case.

[patrickaoude]

mjang2000, I had similar issues.

Please take a look at my pull request and see if it helps: https://github.com/rajewsky-lab/novosparc/pull/21

[nukappa]

@mjang2000 @patrickaoude Thanks, we'll check this.

[enessenel]

https://github.com/rajewsky-lab/novosparc/pull/21 is merged now and the tutorial is updated with f651f2309732861625a79686618a71f393a8c359 for the correct reconstruction with marker genes. @patrickaoude thanks for the contribution!