Reply to: a balanced measure shows superior performance of pseudobulk methods in single-cell rna-sequencing analysis

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    The aim of the publication "A practical solution to pseudoreplication bias in single-cell studies" was to address a need to reduce the number of studies that do not account for within-individual correlation and report astronomically false associations1. The issue is a statistical hypothesis testing question, and the perspective is influenced by the theory underlying the analysis of correlated data2-4. The authors concluded that pseudobulk methods "are only slightly underpowered relative to mixed effects models when there is balance in the numbers of cells per individual, not as well powered as mixed . . .

     

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