Question: Errors during KLD calculation with zero-count genes in DeMAND
gravatar for Jesse Dabney
10 months ago by
University of Oxford
Jesse Dabney0 wrote:

Hi, I've been encounter errors during the KLD calculation steps, specifically in the KLD2D function. As far as I can tell, the problem occurs when one sample condition (eg DMSO) has an abundance of zero counts, leading to tied ranks and 0-value bandwidths. Should these genes be filtered out? I am hesitant to do this since some of these genes have high counts in the treated samples, suggesting that they are affected by treatment. Are there any other options or workarounds?

software error demand • 161 views
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