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Pseudotime construction #207

Open ngvananh2508 opened 1 year ago

ngvananh2508 commented 1 year ago

In the part 13.4.4 Pseudotime construction, there is a paragraph: The differentiation hierarchy in bone marrow is well understood. However, it is only know that the developmental process starts in the form of hematopoietic stem cells but not at which cell exactly in the corresponding cluster in our dataset. To identify a putative initial cell, we study the individual diffusion components. We identify the stem cell with the most extreme diffusion component in one dimension (in our case dimension 3).

Can anyone please instruct me how we know that the most extreme diffusion component is dimension 3?

I am grateful with your help.

WeilerP commented 1 year ago

@ngvananh2508, a priori, you do not know. You will have to look at different pairs of diffusion components to identify the appropriate one.

ngvananh2508 commented 1 year ago

Can you please expound more about this? How can I get this information? I am sorry I am not familiar with non-linear dimensionality reduction. Does it have a diffusion value like the singular value in SVD?

Or can you please suggest to me some documents to study more about this?

Thank you very much!