marker file have 30 clusters

48 views

Skip to first unread message

Jin Ye

unread,

Aug 25, 2019, 9:56:15 AM8/25/19

to garnett-users

Dear Garnett developers,

I have a maker file that has 30 cluster and a dataset with 38,000 cells. However, when I tried to train the classifier with this dataset, in the error message it says that I don't have enough cell for any cluster. If I use less cluster in the marker file (~10), it will work. May I ask what can I do in this case?

And can I use the same dataset for both training dataset and classifying dataset since it is very difficult to find similar exiting dataset? Technically it's possible but what would be the potential disadvantages?

Looking forward to your reply!!

Best,

Jin

Hannah Pliner

unread,

Sep 11, 2019, 1:20:48 PM9/11/19

to garnett-users

Hi Jin,

I'm not sure why that would happen. What does your "check_markers" plot look like? I'm wondering if one of the cell types in your 30 cell type group is conflicting with the other cell types.

We've found that training and classifying on the same dataset works fine so long as you have good markers.