When I run `zlm` with several clusters, how to compare 1 cluster versus all the others?

RGLab / MAST

Tools and methods for analysis of single cell assay data in R

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When I run `zlm` with several clusters, how to compare 1 cluster versus all the others? #165

Closed danli349 closed 3 years ago

danli349 commented 3 years ago

When I run zlm with several clusters (I have clusters 1-7), how to compare 1 cluster versus all the others?

zlmCond <- zlm(formula = ~leiden_r0.3 + n_genes, sca=sca, method = "glm")
1_vs_others <- summary(zlmCond, logFC = TRUE, doLRT = 'leiden_r0.31')

Error Term(s) 'leiden_r0.31 ,' not found. Terms available: (Intercept) , leiden_r0.32 , leiden_r0.33 , leiden_r0.34 , leiden_r0.35 , leiden_r0.36 , leiden_r0.37 , n_genes

amcdavid commented 3 years ago

Please follow the instructions in the README and post your programming questions to support.bioconductor.org.