Open daniel-wells opened 7 years ago
Hi Daniel,
Thanks for catching this. The reason for this behaviour is that if all your genes were transient then PC1 wouldn't correspond to anything like "true" pseudotime, whereas PCA-ing only the switch-like genes will still approximate pseudotime. Ways to fix this I would envisage as
In any case, Stan with HMC is normally efficient enough that initialising randomly gets you back to the "truth", whereas Stan with ADVI is obviously sensitive to init.
Open to suggestions,
Thanks,
Kieran
Hi Daniel,
Thanks for catching this. The reason for this behaviour is that if all your genes were transient then PC1 wouldn't correspond to anything like "true" pseudotime, whereas PCA-ing only the switch-like genes will still approximate pseudotime. Ways to fix this I would envisage as
In any case, Stan with HMC is normally efficient enough that initialising randomly gets you back to the "truth", whereas Stan with ADVI is obviously sensitive to init.
Open to suggestions,
Thanks,
Kieran
Ah I see, I think random initiation seems like a good option - simple and unrestrictive.
Firstly thanks for adding the transient option!
However, when response_type="transient" i.e. no genes are designated switching svd throws an error:
Presumably this is due to attempting prcomp on no genes
https://github.com/kieranrcampbell/ouija/blob/1ebc4ea8e6fd118600969eefaefa13da20c18a4e/R/ouija.R#L170
Perhaps just do a pca of the full Y?
Also in the readme the data is called synth_gex rather than example_gex.