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GreenleafLab / MPAL-Single-Cell-2019

Publication Page for MPAL Paper 2019
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nn_index in scRNA-Projection-UMAP.zip is empty or not compatible with uwot 0.1.8 and RcppAnnoy 0.0.16 #22

Open wangmeijiao opened 4 years ago

wangmeijiao commented 4 years ago

Dear Granja

It is quite a smart idea to apply the 'uwot_transform' to in situ projection of new data (disease sample of both single cell or bulk datasets) to a already calculated umap graph. This method, which is named 'LSI_projection' is exemplified in your script scRNA_02_Cluster_Disease_w_Reference_v1.R. However, when loading the saved umap model file from a tar file in 'scRNA-Projection-UMAP.zip', it complained for the unloaded nn_index. I looked into this issue further by run the load_uwot() code step by step and found a error message "Index size is not a multiple of vector size: Success (0)". and if applied model$nn_index$getNTrees() , I got zero. But , the nn1 file is not empty. As I described above, it seems that either the nn_index is empty or is not compatible with my R enviroment.

Help!

Meijiao

1226235 commented 3 months ago

Hello Meijiao,

I am facing the same problem now and the error on my side is also "Index size is not a multiple of vector size: Success (0)". Have you figured it out? Do you know their R configurations? Thanks in advance!!