Using single cell data from different sources as input

[Qirongmao97]

Hi,

We are trying to use single-cell data from different sources as input for CARD to do the deconvolution. Since the input for CARD is raw counts. I was wondering if you know how well would CARD deal with the batch effects when the single-cell data input is from multiple sources.

Also, if it is possible to use the batch effect corrected expression data as input for CARD, thanks!

[YMalab]

Hi @Qirongmao97,

Thank you for your question.

In both our simulations and real data applications (for example, the PDAC dataset), CARD performs very well with different scRNA-seq references and is robust to the choice of reference. Empirically, it is possible to use batch effect corrected single-cell expression data as a reference as long as it is all non-negative. Thanks!

Best, Ying