NaN values when computing the kernel lead to inability to find t-optimal MATLAB.

[ElenaMerinoTejero]

Hi,

I want to impute a data set X (9082 genes x433 cells) using MAGIC in Matlab.

When running run.MAGIC(X) it results in the following error:

Unrecognized function or variable 't_opt'.
Error in compute_optimal_t (line 62)
disp(['optimal t = ' num2str(t_opt)]);

When running MAGIC with a particular t imput:

[pc_imputed, U, pc] = run_magic_original(X', 'k',30,'a',10,'t',20,'npca',20).

The resulting pc_imputed is a matrix full of NaNs and P and K have some NaNs too. I think this is due to some zero values when calculating kdist and epsilon in the following manner:

[idx, kdist]=knnsearch(data_pc,data_pc,'k',k_knn,'Distance',distfun);
epsilon=kdist(:,k+1);

Why are there NaNs in the pc_imputed and is there any suggestion you can give to find suitable pc_imputed for my data set?

Thanks in advance 🙏.