How true it is? Are the loading controls (actin, GAPDH etc.) or internal controls expressed equally between the conditions? especially between different cell types (between a muscle cell and a neuron cell for example)? I would like to know if I have to compare a normal tissue and a inflamed tissue (inflamed tissue generally infiltrated with other immune cells). And also the liver specific protein expression analysis could be inaccurate due to the presence of other cells in case of inflammation. How does somebody proceed in this case?
This is always a tricky situation when you compare the expression levels of the housekeeping genes among different cell or tissue types. For example, GAPDH is required more in the cells with higher energy requirement and hence are expressed more there. Then there is Beta-Actin which exists in two forms: F-Actin and G-Actin which is in constant equilibrium. There are few links in the context of your question. One very recent infact. May be it will help you
https://www.ncbi.nlm.nih.gov/pubmed/27297043
Article ??-Actin is not a reliable loading control in Western blot analysis
I second Vikrant. The best option is to analyze the expression of a larger group of presumed reference genes under the variety of the experimental conditions and then find the (sub-)group of genes that show the most similar expression pattern across the conditions. Then ideally use all these genes as reference (loading control).
Additionally to Jochem's answer:
Reference genes should always be established before running an (RT-)qPCR experiment.
The analysis of the stability of the tested reference genes can be done with GeNorm or an intergrated version of GeNorm in a qbase+ software.
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