single-cell transcriptomics and bulk proteomics data integration

Question

[frarodmar17]

I would like to perform single-cell RNA-seq and bulk proteomics combined analysis, but the samples are not the same in both studies. I am not sure if I can use a specific software to perform the integration, or if I should integrate Differential Expression Analysis results in both cases to perform the analysis (in this case I could integrate p-values and fold-change values of both analyses). What would you recommend? My objective is to perform a multi-omics analysis, and it is not to have a combined data matrix.

[colindaven]

Don't you think single cell and bulk rna-seq are inherently different things ? Why would you do single cell if they were not ?

[frarodmar17]

They are different studies and experiments. What I want to do is to analyse both perspectives.

[AB]

Not sure what your aim is, but you could analyze both separately and look at correlation . For instance, get the differentially expressed genes from your single cell and differentially expressed protein from your proteomics analyses and do a correlation test