Separate or pooled analysis for different experimental conditions

[tt2190]

Hi,

Thank you for developing this great tool!

I was wondering if I should run scFEA separately on the different scRNAseq data from different experimental conditions or I can simply run scFEA on a concatenated expression matrix to compare the fluxome between conditions.

For example, to generate Figure 4 (APEX1-KD vs control), did you run scFEA separately on 1) Normoxia Control, 2) Normoxia KD, 3) Hypoxia Control and 4) Hypoxia KD and then compare the flux? or did you run scFEA on a concatenated expression matrix that includes all four conditions and then compare the flux?

Given scFEA tries to minimise the overall flux imbalance across all input cells, the former approach (run scFEA separately and compare the flux) sounds more reasonable than the latter, but I am not sure if the flux estimates from separate scFEA runs are comparable.

Thanks,

[98wmw]

Hi,

Thank you for developing this great tool!

I have the same question with you.I am confused if my data containing pre-treatment and pro-treatment could estimate separately,or I should estimate together. which method runs are comparable?

Thanks,