Hello everyone! I am dealing with a scRNA-seq dataset having cells (SKOV3 cell culture) in 4 different conditions (2 levels of treatment). There are some biases: one of the conditions has 10 times more cells than others, whereas 3 others had doublets which have been filtered out.
Basically, clustering gives me the same result as sample annotation. My primary interest was detecting marker genes between clusters and/or conditions. However, running FindAllMarkers gives me a table where for each cluster there is a strong bias towards either upregulated, either downregulated genes . I tried to sample the biggest condition so all of them would be of the same size, but it didn't fix my problem.
Is it a common problem with single-cell data? Is it possible to fix it? Any advices would be appreciated.
Thanks!!