In terms of limma/edgeR usage, this seems to be a weird question. However, my question is for such situation: Assuming I collected lots of single cell datasets, and I have a set of candidate genes. What I want to ask/test is that: Is there some genes only expressed in some cell types ?
I can build linear model use limma and test whether some genes differential expressed between different types of cells.
fit = lmFit(y, design = model.matrix(~ 0 + celltype + other_covarites))
But here I change the null hypothesis to a gene is not expressed in all cell types, it seems that I need a hypothesis test to test on mean expression above some threshold but not logFC. I am not sure I asked the right question and is that possible to do that ?
Any advice would be appreciated.