I am trying to analyse some single cell RNA seq data with MAST, currently I'm using an edgeR pipeline and I cannot work out how to properly test a contrast in MAST.

The experimental setup is a 3x2 with 3 strains and 2 conditions, I'd like to test differential expression between the conditions within each strain. I have set up a "strain-condition" style factor for my samples and I'm using a `~0 + group` design. My understanding was that I could use

    zlm_output <- zlm(~0 + group, x)

    summary_contr <- summary(zlm_output, doLRT = c(1, -1, 0, 0, 0, 0))

To test my contrast of interest. However this gives me the following error

    Error in logFC(zlmfit, contrast0, contrast1) : 
      Assuming comparision to intercept, but I can't figure out what coefficient that corresponds to.  Provide `contrast0`.

Could someone guide me in the correct usage of this package for testing contrasts?

1. You can fit such a model a "cellmean model" (zlm_cellmean = zlm(~ 0 + group, x)) though it is possibly a little less statistically efficient [1] than using contrasts that explicitly includes an intercept:

   ## assuming you manually crossed strain and condition to get group
   zlm_dummy = zlm(~strain*condition, x)
   ## Not so friendly
   contrasts(colData(x)$strain) = "contr.sum"
   contrasts(colData(x)$condition) = "contr.sum"
   ## classical anova -- maybe this is what you want?
   zlm_sum_to_zero = zlm(~strain*condition, x)
   

2. The summary method (?'summary,ZlmFit-method') supports contrasts offered as a character vector, which seemingly doesn't cover the zlm_cellmean case.

3. To test contrasts symbolically or numerically you may offer them to lrTest

   lr_anova <- lrTest(zlm_cellmean, Hypothesis('groupLevel2 - groupLevel1'))
   # columns give a set of contrasts. more than one column means a joint test.
   lr_anova2 <- lrTest(zlm_cellmean, as.matrix(c(1, -1, 0, 0, 0, 0)))
   all.equal(lr_anova, lr_anova2)
   

​[1] This is due to a heuristic in the coefficient shrinkage that shrinks "intercept" columns less than "treatment" columns.