Good question, I would probably calculate deltaDeltaCt values for each sample by subtracting the average of all deltaCt values from each individual Ct value. Then calculate RQ as normal (2^-(deltaDeltaCt)) and plot those for each sample.
I think this approach would be good to show differences in expression of the target gene between samples since ddCt is calculated relative to the group mean, but I am curious what others will recommend!
Simply show the dCt values. Don't make any fuss with additional calculations, normalizations or whatever. You will see (and you can test) in which group the mean dCt is higher or lower.
For examples, see
Figure 7 in https://www.atsjournals.org/doi/10.1164/rccm.201401-0037OC?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed
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