Imputing integrated data

[kvshams]

Hi,
Thank you for the nice tool. Is there any way to use ALRA in integrated data?. Currently if we use ALRA, it seems to be masking the difference in expression between treatment and control. One way would be the splitting the object and do ALRA separately, but while combining back the object, the alra assay is not preserved.

Thanks

[linqiaozhi]

Hey @kvshams, thanks so much for your interest in ALRA! The question of whether to do ALRA before or after integration is a good one; we need to investigate it further before we have a definitive answer.

This paper had good results by doing ALRA on the merged dataset and then running Harmony to correct for batch effect between the batches. Their code is available in that link, but they did not use Seurat. I presume something similar would not be hard with Seurat, though.