Thank you for sharing all the information. I was able to reproduce the exact results using your Matlab scripts but couldn't reproduce them in my R implementation. I noticed a mistake in your scripts:
Cell_Ids = txt(1,2:end);
The Cell_Ids are shifted, which affects the subsetting by conditions (d0, d3, and d9). The resulting clusters are quite different after correcting this mistake. I observed 2 distinct clusters instead of 3 and memberships are different with the ARI index (~0.25).
Thank you for sharing all the information. I was able to reproduce the exact results using your Matlab scripts but couldn't reproduce them in my R implementation. I noticed a mistake in your scripts:
Cell_Ids = txt(1,2:end);
The Cell_Ids are shifted, which affects the subsetting by conditions (d0, d3, and d9). The resulting clusters are quite different after correcting this mistake. I observed 2 distinct clusters instead of 3 and memberships are different with the ARI index (~0.25).
Correction: Cell_Ids = txt(1,1:end);
Best regards, Enes @nslavov