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I am writing an article where I describe real-time PCR experiments. My collaborator, after reviewing the article, consistently replaced the word "parallels" with "replicates". Are they not synonymous?

I prefer the word parallel, because, in the context of PCR, it implies that these three identical experiments were performed in the same real-time PCR run (and not consecutively).

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Can you give a couple of examples of the text in question? –  kmm Feb 28 at 17:07
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Replicates is certainly more common usage in general. If you wish to emphasise that these replicates were performed in the way that you describe perhaps say "replicates run in parallel". –  Alan Boyd Feb 28 at 17:09
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Parallels is not as good a word imho - you can run several concurrent experiments and call them run in parallel. replicates are the same experiment. –  shigeta Feb 28 at 19:30
    
In any case, parallels won't work, you want experiments run in parallel which is not the same thing. Parallels cannot be used that way. –  terdon Mar 2 at 18:11
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The explanation I got when learning how to do qPCR was that you need run both replicate experiments and parallel experiments to get publishable data.

Replicates (or biological replicates) would be qPCR runs on independently collected samples. That does not count your control vs your experimental groups. So for my work I had to collect 3 sets of control tissue and 3 sets of experimental tissue from independent sets of animals (in my case 3 generations but for mammalian work I think three different animals would be ok).

Parallel does imply that you ran the the samples together in the qPCR machine. I think the standard is that for each sample in a particular replicate you need to run three qPCR reactions in parallel. So in total you need to run 9 wells of qPCR reactions for each test group.

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Technical replicates show that the technical integrity (pipetting, master mixes, detection) is consistent, which biological replicates show that the effect you are measuring is genuine and happens not by chance. Usually you do three technical replicates per run and sample and repeat an experiment three times independently. –  Chris Mar 1 at 10:25
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