Differential analysis on deconvolved cell type expression

[ishagd]

Hi,
I ran BayesPrism for bulk RNAseq data from two conditions: pre and post-treatment separately.

What is the best way to perform DE analysis for a specific cell type (e.g. CD4 T cell) between pre and post-treatment timepoints using this gene expression matrix output?

Is using DESeq2 recommended considering the output data is normalized?

Thanks in advance.

[tinyi]

Hello. To use DEseq2, you should 1) use raw count as input for BayesPrism, and 2) round up the Z matrix to the nearest integer and use it as input for DESeq2 (without any normalization step).

[ishagd]

Great, thank you for your reply!