Hi,

to compare the gene expression level between one or more sample in response to a treatment, a relative quantification such as the delta delta CT method is the gold standard. You qPCR program might even provide you with all the tools needed to calculate relative quantification right from the acquisition data file.  

In your setup, you can compare the cytokine expression between untreated cells and infected cells. Once that you have your relative quantities, make sure to apply an appropriate statistical test if you want to compute the statistical significance (ex. one-way Anova and post-hoc test for the significance and not multiple t test). 

Also, make sure that you have the appropriate number of biological and technical replicates as well as more than one housekeeping genes for normalization. This will ensure a robust and reproducible analysis especially if your are dealing with low or high expression cytokines. 

An absolute quantification is more appropriate for quantify a target that is not relative to anything like the number of viral copy number in a sample. 

Also, when performing qPCR experiements, it is good to refer to the MIQE guidelines that provides a lot of information about experimental set-up and reporting. 

Good luck!

http://www.rdml.org/clinchem.2008.112797v1.pdf

Thank you for your answer. It will definitely help me a lot.  Usually, what is the appropriate number of housekeeping gene that need to be used for normalization? thank you again.

Nicolas provides an excellent answer-it is relative expression between a treatment and control. Normalisation of RNA levels and sufficient replicates are a key point-and the analysis is also important-the use of a post-hoc test like Tukey's is critical.

Thank you for the clarification and I will include all the explanation/answer in the SOP for my experiment.