Error in computing default starting values

[biofunny]

Thanks for your software. I met this error when I run PseudotimeDE::runPseudotimeDE. This error appears only when I use all 3000 genes as input. If using one or two genes, it works well. I'm looking forward to your reply.

[SONGDONGYUAN1994]

Hi,
Thanks for your question. It would be nice if you can give me an reproducible example and the whole error message. I hesitate it is caused by the package fitdistplus: Q&A. Could you determine which gene(s) lead to this error? For example, split your genes into small groups to check which group will have this error. Then I can help you check this. Thanks!

[SONGDONGYUAN1994]

BTW, you can try the fix mode. If it works, the error must come from fitdistplus.

[liuyu988]

Hi, Song!
I'm sorry to disturb you.
I want to use the PseudotimeDE package after merging two seurat objects, and I found the PCA results disappear after merging, however, the reductions must be gained in use, then I wonder that if it's correct to run the 'RunPCA' again .

[SONGDONGYUAN1994]

Hi Yu Liu,
Thanks for your question. I think it is fine to re-run the PCA. This question is more related to Seurat, of course. You need to decide your pseudotime inference pipeline before running PseudotimeDE.