Pierre-Luc
Pierre-Luc
Dear Owen, A few questions: 1) could you tell us whether you installed the bioconductor release of muscat, the devel, or a github branch? 2) what is the `class(counts(sce2))` ?...
Thanks for the precisions; I sent you an invite by email (@ Dartmouth), let me know in case you didn't get it.
Hi @owenwilkins So I'm not actually getting exactly the same error you are getting, but here are the things I had to address to make it work: * I think...
Both issues should disappear in the latest github push (master branch).
That was a typo, should be fixed now. At the moment there's not really an in-built possibility to use non-counts inputs to mmDS. One possibility would be to pretend that...
Hi, If you google around you'll see that this is a major issue that broke dozens of Bioconductor packages (and Seurat as well), I'm afraid there's nothing I can do...
Hi, Thanks for the nicely reported issue. You're using scDblFinder 1.12.0, the current release one is 1.16.0, and the ability to specify which genes to use was added in 1.13.7,...
Hi, What do you mean exactly by "rRNA contamination-related genes"? Whether it's better to do it before or after chiefly depends on what proportion of the variability in those genes...
Ok, I can't say what's best. The fact that it varies across your clusters, unless you think the contamination drives the clustering (i.e. if there aren't big differences except for...
Hi, thanks for reporting this. Until I fix it, what you can do is run the aggregation separately, e.g. this should reproduce what you're trying to do: ``` sce.ag