HVG query vs ref

[Nusob888]

Hi,

Are there any recommendations on how to mismatch/process query datasets where not all HVGs of the reference are within the query?

Should we be zero padding missing data?

[M0hammadL]

Hi, for now i would say zero padding is the best way to do it

[Nusob888]

Brilliant, thanks. Are there any future plans on a more nuanced way to take this into account? Have you found zero padding to influence the transfer certainty?

[M0hammadL]

indeed see supplementary figure in scarches paper, more zeros in query worse integration and thus uncalibrated (un)certainty