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lmweber / diffcyt

R package for differential discovery analyses in high-dimensional cytometry data
MIT License
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Insights into data transformation #58

Open Thapeachydude opened 4 months ago

Thapeachydude commented 4 months ago

Hi,

I was wondering if you have anymore insights/guidance on the data transformation. I have a spectral flow cytometry data set, that a collaborator acquired. I've tried the general 150 co-factor, most markers look Ok this way, but individual ones now have a very weird "negative" smear.

Have you had this issue before and is there any good way to judge the quality of the transformation? (besides just looking at it)?

Happy for any insights!

Cheers

SamGG commented 4 months ago

Hi, diffcyt is not really dealing with data transformation. I don't know which spectral instrument acquired those data, but I think the co-factor is too low. To tune it correctly, follow the discussion and guidance in Liechti et al. , especially fig2 d & e. Best.

Thapeachydude commented 4 months ago

Hi, thanks for the quick reply! That indeed proved to be quite helpful!