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Nanostring-Biostats / InSituType

An R package for performing cell typing in SMI and other single cell data
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Problem on running semi-supervised method on reference matrix from Nanostring-CellProfile-Library #191

Closed Sakura1a2a3a closed 5 months ago

Sakura1a2a3a commented 1 year ago

I am trying to run the semi-supervise method, and I am using reference data Colon_HCA.RData from CellProfile Library linked from Manuscript. I also tried to use ioprofile which is given as example which works well, I am wondering why Colon_HCA.RData would cause an error. Here is what I did:

load("./Colon_HCA.RData") pro <- as.matrix(profile_matrix) select anchor cell... get updated reference......

Screenshot 2023-06-19 at 6 13 52 PM Screenshot 2023-06-19 at 6 14 59 PM Screenshot 2023-06-19 at 6 15 23 PM

I am wondering why I can simply use ioprofile which would work, but I get an error when I use Colon profile. What should I do if I want to use profiles from Nanostring Profile-Profile -Library?

patrickjdanaher commented 5 months ago

I suspect this has something to do with the very small values input for n_phase1 etc.

I'll change the vignettes to suggest higher values.