Comments (1)
nargesr
commented on July 26, 2024
Hi,
so WGCNA starts finding modules by calculating the correlation between each pair of genes and then finding the soft threshold to scale the calculated matrix to have a scale-free network and define modules based on the dissimilarity matrix.
If your input contains only 0 and 1, it would affect the correlation part and you might end up with a bunch of Nan values based on the ratio of zero and one so not sure how you want to interpret those.
In the end, I think it might still be worth giving it a shot but you might see too many warnings like "Some correlations are NA in block ..." when you call findModules() function, and if that's the case I would suggest looking for another tool that designed to work on boolean matrices.
Hope I can answer some of your questions
Best,
Narges
from pywgcna.
Related Issues (20)
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