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lorenzobonaguro / cyCONDOR

Flow cytometry analysis workflow. The aim of this project is to provide an intuitive workflow for the analysis of high-dimensionality cytometry data in R.
https://lorenzobonaguro.github.io/cyCONDOR/
GNU General Public License v3.0
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changing results for emmeans test in frequency_anova_test #10

Open c-kroeger opened 1 month ago

c-kroeger commented 1 month ago

P-values are changing depending on which cluster/cell types are provided to the emmeans test after filtering the anova results. Seems like emmeans_test interprets the grouping by cluster/cell type strangely.

lorenzobonaguro commented 2 weeks ago

Hi Charlotte, Thanks for pointing out this issue, The changing is pvalues is because emmeans_test() interprets the variable provided in group_by(variable) as a covariate of the model and it calculates expected groups means after controlling for the covariates.

We are currently looking into this issue and plan to release a definitive fix with the next cyCONDOR version (0.2.1). Updates will follow on this thread.

Thanks again @c-kroeger and @skmueller for looking into this!