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Adding comparisons in Hurdle model uses the same interface as ANOVA/LIMMA-trend/LIMMA-voom. Start by choosing a factor or interaction from the Factor drop-down list. The levels of the factor or interaction will appear in the left-hand panel. Select levels in the panel on the left and click the > arrow buttons to add them to the top or bottom panels on the right. The control level(s) should be added to the bottom box and the experimental level(s) should be added to the top box. Click Add comparison to add the comparison to the Comparisons table. Only comparisons in the Comparisons table will be included in the statistical test. 

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Hurdle model produces a Feature list task node. The results table and options are the same as the GSA task report except the last two columns (Figure 3). The percentage of cells where the feature is detected (value is above the background threshold) in different groups (Pct(group1), Pct(group2)) are calculated and included in the Hurdle model report. 

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Applies shrinkage to the regression coefficients in the discrete (logistic) part of the hurdle model. Default is Enabled. The initial versions of MAST contained a bug that was fixed in its R source in March 2020. However, for the sake of reproducibility the fix was released only on a topic branch in MAST Github [2] and the default version of MAST remained as is. To install the fixed version of MAST in R, run the following R script.

# Uninstall the default version of MAST, if it's installed.
remove.packages("MAST")
# Install devtools, if it's not installed yet.
library("devtools")
install_github("https://github.com/RGLab/MAST/tree/fix/bayesglm")
library(MAST)

In Flow, the user can switch between the fixed and default version by selecting Fixed version or Default version, respectively. To disable the shrinkage altogether, choose Disabled.

References

[1] Finak, G., McDavid, A., Yajima, M., Deng, J., Gersuk, V., Shalek, A. K., ... & Linsley, P. S. (2015). MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. Genome biology, 16(1), 278.

[2] MAST topic branch that contains the regression coefficient shrinkage fix:

https://github.com/RGLab/MAST/tree/fix/bayesglm

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