Running SCALE on Multiple Samples Together

[annachernysheva179]

Hi,

I found your preprint very interesting and would like to try SCALE.

I have a question:

• Should SCALE be run on each sample individually, or is it possible to run it on all samples together? Does it require specifying batches/samples somewhere then?

Thank you!

[dschaub95]

Hi,

The current implementation of SCALE does not support multi-sample integration, but we are actively working on supporting it. I will get back to you early next week and provide a vignette with different options for that case. So, for now, you have to apply it to each sample separately.

Best
Darius

[dschaub95]

Sorry for not getting back to you earlier... I have been working on this for some time, but have not yet achieved satisfactory results on diverse datasets, so we will need some more time to provide a robust multi-sample integration feature.