Pierre-Luc
Pierre-Luc
Please provide a session info
What is your Bioconductor version? (run `BiocManager::version()` ) It seems your `beachmat` version is from 3 years ago, which suggests an old bioconductor installation (bioconductor will always install the package...
Will close this unless you can reproduce on newer versions.
Hi, if you use `retType="table"`, the output will be a data.frame containing all the variables for both real cells and artificial doublets. Pierre-Luc
Hi, You can simply pass the name of the `colData` column (e.g. `"CDR"`) to the `covs` argument of `muscat::mmDS`. Note that it's better to use something scaled like the CDR...
The correct way to refer to the coefficient would be "group_idHealthy", assuming that it's not the base (i.e. first) level of the factor. You can see the coefficients with `colnames(model.matrix(~group_id,...
Hi, under the hood it is, but this is essentially added by `mmDD` to the model you specify. I'm not sure but I don't think model.matrix can handle random effect...
No, my point was that standard significance testing for mixed models does not test the significance of random effects. In other words: ```{r} coef(summary(lmer(y~(1|sample)+x))) ``` doesn't perform any testing on...
Hi, could you share the data for a minimal reproducible example? And can you tell us which exact muscat version you're using?
So the strange values using `vst` come from `sctransform` : it seems like there is a cap on the maximum values. I guess however this shouldn't affect the results very...