Closed davidsebfischer closed 6 years ago
Dear David,
I'm not sure what is causing the error you are receiving, I suspect it is to do with the low numbers of droplets where the code expects hundreds of thousands. However, I am not confident that the assumptions of the method will hold true for plate based data, so would not recommend trying to use our method on plate data.
So I'm afraid for the moment using SoupX on plate data is unsupported.
Hi SoupX team!
I would like to use SoupX on plate-based scRNAseq where we included empty wells (so that we can use them similar to empty droplets). I guess there is no reason to assume that the model would not work on this type of data?
Attempting this, I called the SoupChannelList constructor directly with my data (as the 10x input handling function is not appropriate here) and I got an error in inferNonExpressedGenes().
Do you have any intuition as to why this could happen? I cannot share the data unfortunately. Session info for this example:
Thanks for your help! David