I ran some experiments to quantitatively evaluate the expression of the products of a few genes in some cell lines. For calibration, I used the positive cell line which reported full expression of the target gene. Since the expression of target gene in our cell lines is much lower than its expression on positive cell lines, we have a problem with data presentation, especially in the form of a diagram. Any suggestions?
Use the lowest expression sample as your calibrator. All data will be positive
I would rather go for the logarithmic representation as suggested above. But then I have a question: why do you use an external reference to do quantitative gene expression? What is/are this/these cell line(s)? Cells transfected with your gene of interest? In my mind, it would be better to use a reference gene with comparable expression levels (known as "housekeeping gene") in all your cell lines. In this case, it will also be good to choose a reference gene with expression levels close to the expression levels of you genes of interest, in order to avoid normalization by a huge factor which will flatten any potential difference in gene expression.
Good luck with your experiments,
Fabrice.
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