Bimodal data?

[Jan Vincent B. Beltran, Ph.D.]

Hello! I would like to ask for your advice/opinion about my results.

I integrated 2 independent scRNA-seq datasets from different studies using Seurat and then performed scGen. On the figure attached below, it appears that the R condition has 2 modes, which makes the prediction somewhere in between those modes.

I wonder if you could give me advice on how to get a workaround on this, like whether this figure gives an insight that the two datasets are not compatible to be integrated to begin with. Or are there other tools which I can use to investigate this to resolve my prediction inaccuracy?

[Ali Rassolie]

Are you using two independent datasets from different studies as input?

[Jan Vincent B. Beltran, Ph.D.]

Yes, 2 independent datasets from 2 different studies.

[Jan Vincent B. Beltran, Ph.D.]

Hello. Any comment on this?

[M0hammadL]

Hi @levinhein

I think this issue will be soled by using a zero-inflated model in the output which we are not using at the moment and assume the data is uni modal gaussian.