Open MayaCyTOFnewbie opened 2 years ago
Hi again,
can anyone help?
thanks again,
Maya
Hi Maya, did you figure this one out? I'm facing the same issue.
I'm not fully sure (I'm guessing), but often model.matrix()
makes a modification to the column names with conditionXX
when using ~0+condition
, but I would need to check it.
If your code is like above, can you give the output of design
and contrasts
to make sure they match up correctly?
Hi!
thank you for this package and for the useful tutorials!
I am working on CyTOF generated data, where I have four groups of treatments, and I want to make three pairwise comparisons treatmentA to treatmentAB treatmentC to treatmentCB treatmentCB to treatmentAB
How do I create a design matrix and contrast?
this is what I did, but I am not sure it was the correct thing to do
my results don't show the different comparisons and without any statistical value
thanks!
contrasts <- makeContrasts( treatmentAB-treatmentA,treatmentCB-treatmentC , treatmentCB -treatmentAB , levels=colnames(design))
da_res1 <- diffcyt(sce, design = design, contrast = contrasts, analysis_type = "DA", method_DA = "diffcyt-DA-GLMM", clustering_to_use = "merging")
rowData(da_res1$res)