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BiomedicalMachineLearning / stLearn

A novel machine learning pipeline to analyse spatial transcriptomics data
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stlearn CCI is not working for multiple slides? #270

Closed howtofindme closed 6 months ago

howtofindme commented 9 months ago

Dear developer, Thanks for your wonderful jobs! I have learned from your tutorials in Integration_multiple_datasets section. But I found the integrated object is not working correctly for stLearn Cell-Cell Interaction Analysis when I run the following codes using the integrated data:

Basic normalisation

st.pp.filter_genes(data, min_cells=1) st.pp.normalize_total(data) # NOTE: no log1p for CCI image you can see the data.var becomes zero.

duypham2108 commented 9 months ago

You should make sure 2 slides (samples) have to have the same set (or subset) of genes

howtofindme commented 8 months ago

You should make sure 2 slides (samples) have to have the same set (or subset) of genes

Yes, you are right,solved, Thanks