I need help with some qRT-PCR error bar calculations. I have carried out all of my qPCR with my gene of interest and of my housekeeping gene and have calculated my fold-changes for my gene of interest with the delta-delta-Ct calculation. However putting error bars on my graph showing the fold-changes is confusing me. What data should I be using to calculate this? I can't use the normalized Ct values as this is not correct for fold-changes and when I convert my Ct values (for my calibrator and experimental) using the delta-delta-Ct calculation and then get the SE for that my error bars are bigger than my fold-change. Can anybody shed some light on this and where I am going wrong? I can't use the software that comes with the qPCR machine as it is getting confused with how my plates are arranged.
Thank you in advance!