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KrishnaswamyLab / SAUCIE

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Unique cluster #9

Closed fedeago closed 5 years ago

fedeago commented 5 years ago

Hi, i am trying to use saucie to find cluster, i can run the code but it fin only one cluster. I checked, and after log-transforming the data the maximun is near +11 and the minimun near -4. Someone know why could this happen?

mattamodio commented 5 years ago

Hi there, thanks for trying out SAUCIE! The most common reason for that is if the default hyperparameter choices are not optimal for your dataset. I would try reducing the amount of the clustering coefficient, instead of SAUCIE(lambda_c=.1, lambda_d=.2), maybe try SAUCIE(lambda_c=.05, lambda_d=.2) or also increasing the intra-cluster distance coefficient, like SAUCIE(lambda_c=.05, lambda_d=.4). Hope that helps!