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I'm recently following this tutorial to get familiar with the functions in the MUDAN package.
However the embeddings from Rtsne:: Rtsne could not be reproduced very well: if it is run respectively at two time points, the number of the clusters is consistent but the shape and/or the locations of the clusters/cells might be different. It might make the tutorial a little bit confusing, especially for the learners.
To address this and to make the results more 'reproducible', adding 'set.seed()' might be an efficient way. (e.g., https://satijalab.org/seurat/v3.1/interaction_vignette.html) In this case, the coordinates of each cell will be constant between different sessions.
Thanks,
JY
The text was updated successfully, but these errors were encountered:
Hi,
I'm recently following this tutorial to get familiar with the functions in the MUDAN package.
However the embeddings from Rtsne:: Rtsne could not be reproduced very well: if it is run respectively at two time points, the number of the clusters is consistent but the shape and/or the locations of the clusters/cells might be different. It might make the tutorial a little bit confusing, especially for the learners.
To address this and to make the results more 'reproducible', adding 'set.seed()' might be an efficient way. (e.g., https://satijalab.org/seurat/v3.1/interaction_vignette.html) In this case, the coordinates of each cell will be constant between different sessions.
Thanks,
JY
The text was updated successfully, but these errors were encountered: