It is a bit too generic a question..

If you had an absolute quantification or CNV ddPCR assay which will provide the % of positive cells, you can compare the positive fraction with those resulting from flow cytometry. You will need at least a duplex assay with an unknown sequence and one normalizer with known ploidy to calculate the copy number per cell. For flow cytometry, if your target is a stainable surface marker or a fluorescent protein, you can easily find out the % of positive cells. For absolute quantification of the cell number, you should use counting beads or a peristaltic pump cytometer (is. Beckman Cytoflex) to allow volumetric cell counting.