I have run a qPCR experiment investigating a variety of genes for a time series of samples and was wondering how to calculate my ΔΔct values in relation to this. I have control genes for each sample (gapdh) which vary slightly for each and I have a variety of genes I am testing the expression of. When calculating ΔΔct values I know you are meant to do it relative to your control gene (ie gapdh) and then relative to your control sample. However as I have a time series I do not have a specific control sample as each gene expression pattern varies from time point to time point. Any ideas how to do this please?