stlearn CCI is not working for multiple slides?
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howtofindme commented
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
you can see the data.var becomes zero.
duypham2108 commented
You should make sure 2 slides (samples) have to have the same set (or subset) of genes
howtofindme commented
You should make sure 2 slides (samples) have to have the same set (or subset) of genes
Yes, you are right,solved, Thanks