Saket Choudhary

If I understand it correctly, you do not want to integrate the control and drought datasets - is that correct? For now I would recommend integrating all of them together....

In this case, you could merge => Run SCT => Integrate, assuming the sequencing depths are comparable across the merged samples. If that is not the case, you could caculate...

Hi @vitkl, sorry for the delayed response. This is currently not supported, but we are considering supporting related features in a future version of Seurat.

Can you post the full code here?

Hi @AmelZulji, what version of Seurat are you currently using? This works fine for me with Seurat v4.1.0 and SummarizedExperiment 1.14.1: ```r pbmc_small_sub

Thanks, I can confirm that I now receive an error with SummarizeExperiment 1.24.0. We will have a fix soon.

Thanks @exaexa for keeping us informed. We will check with the latest version once it is up.

Are the input matrices exactly the same? You can generally have multiple gene ids associated with a gene symbol. Also, the only difference I can see above is in the...

Thanks for the request - it can definitely be parallelized. I will look into it.

Can you update to a more recent version of sctransform? I am unable to reproduce this with the latest version: ``` data