Open liz-is opened 6 months ago
Hi @liz-is, apologies for a long silence.
Its hard to answer this wo seeing design model matrix (can you share it perhaps?) - but naively i would assume that you have some redundancy in your matrix. I wonder if the covariates you include n your matrix create such design? So yeah, if you could share with me your design and specifically model matrix you get from this design, I could maybe help a bit more?
So maybe changing the formula to avoid the redundancy would be the way to go.
Hi,
thanks for the cool package, it's been useful and easy to use so far!
I have a control condition and three "treatment" conditions, and I'd like to compare each treatment to control. My condition metadata column is set up as a factor with four levels. I can't figure out how to specify the appropriate contrast as an argument to
de_test_neighbourhoods
. The documentation forde_test_neighbourhoods
says this should be a string, and to look at the edgeR docs for the syntax. In the edgeR docs I see two ways of specifying contrasts: usingmakeContrasts
, or as a numeric vector.I tried
contrasts = "Treat1-Control"
by extrapolating from themakeContrasts
syntax, but this gave me the following error:Any suggestions about what I should be putting instead? I really couldn't find any section in the edgeR docs where they specify contrast as a string. A section reference or an example would be really helpful.