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.
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