auto-rescaling of reference profiles

[patrickjdanaher]

Background

A new reference profiles matrix will be subject to platform effects. It could be necessary to re-scale its rows (genes).

Proposal

Basic approach: use residuals from an initial fit to re-scale the reference profiles.

Option 1:

1. run insitutypeML (fully-supervised)
2. get residuals

Option 2:

1. add all cells together to make a single bulk profile
2. use spatialdecon to deconvolute it from the ref profiles
3. get residuals

Work plot

• Get a good test dataset. The Will Hwang PDAC profiles are promising.
• Try both the above approaches.

[patrickjdanaher]

implemented