Lowest suggested value for lambda?

welch-lab / liger

R package for integrating and analyzing multiple single-cell datasets

GNU General Public License v3.0

380 stars 78 forks source link

Lowest suggested value for lambda? #279

Closed lucygarner closed 10 months ago

lucygarner commented 1 year ago

Hi,

Is there a minimum value that you suggest for lambda? I tested from 5 down to 0.001 using RunOptimizeALS from SeuratWrappers and it didn't seem to affect the integration much.

Best wishes, Lucy

cgao90 commented 1 year ago

Hi Lucy,

In most cases, lambda doesn't have a significant impact on RunOptimizeALS. Normally we set lambda = 5 by default in analyses. When it comes to online iNMF, it can have a larger effect at times.

Best,