Thank you for the video tutorial! It helped me a lot. I am also confused on how to choose a threshold though... When do we say that the threshold is not good and we need to change it and how? Thanks again :)
Thanks for the great video again! Do you have any preference between tSNE and UMAP clustering methods? I've noticed many people seem to use them interchangeably, so I was wondering if some people are insidiously cherry picking the best visualization on their results or one is actually better than the other in some cases.
Thats a great question and I'm not sure there is a clear answer. Typically I almost only use UMAP now. Theoretically UMAP is newer and "better". But recently I read something saying TSNE is better. I'm sure you can find people arguing strongly one way or the other like it is the biggest difference in the world. But at the end of the day they really do the same thing. Typically, the clusters are a little tighter with UMAP and I think this looks nicer. I'm still going to stick with UMAP until I see a good reason not to.
I would say the only important consideration is consistency. If you make a paper/presentation -- don't arbitrarily switch back and forth between the two
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Thank you for the video tutorial! It helped me a lot. I am also confused on how to choose a threshold though... When do we say that the threshold is not good and we need to change it and how?
Thanks again :)
Nice Video.!but still confused about how to choose threshold🤔
Could you please help how to make a violin plot using AUCell package like you did for dimplot?
Thanks for the great video again! Do you have any preference between tSNE and UMAP clustering methods? I've noticed many people seem to use them interchangeably, so I was wondering if some people are insidiously cherry picking the best visualization on their results or one is actually better than the other in some cases.
Thats a great question and I'm not sure there is a clear answer. Typically I almost only use UMAP now. Theoretically UMAP is newer and "better". But recently I read something saying TSNE is better. I'm sure you can find people arguing strongly one way or the other like it is the biggest difference in the world. But at the end of the day they really do the same thing. Typically, the clusters are a little tighter with UMAP and I think this looks nicer. I'm still going to stick with UMAP until I see a good reason not to.
I would say the only important consideration is consistency. If you make a paper/presentation -- don't arbitrarily switch back and forth between the two