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I've noticed that PCR amplification is commonly done before analyzing the DNA sample with microarrays or biosensors.
However, won't amplification biases or errors mess up the gene expression profile results you get from a microarray? Secondly, does that mean amplification only allows you to get qualitative information from say an electrochemical biosensor? (rather than actual quantitative information about DNA concentration)
Anytime you have PCR in a protocol, yes, you might mess up the quantification. So you do as little PCR as you can, so that it stays in the linear range, preserving the different abundances of templates (qPCR after all is the gold standard for quantifying expression), and you hope that there are minimal PCR biases between templates.
Yes, it does.
That is why you should include positive and negative controls and repeat the experiments multiple time to then average the results.
In general, amplification by PCR is biased by sequence-dependence efficiency. For several reasons (among which GC content, annealing mismatches PCR buffer and the timing and temperatures of the cycling steps) a particular template can be over- or under-estimated.
For example, if one sequence is amplified 10% more than another in one round, it will be 1.1^30 = 17.4 times more abundant after 30 amplification cycles.
Here some literature on the topic:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2292241/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3628873/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129672/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2727727/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4433096/
This doesn't mean that you can't get quantitative information. PCR is used to get quantitative results in many fields of research. You "just" have to be sure you are doing it correctly. Be aware that experimental confounders may mess up your results, so be critical when you analyze your own data.
