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In Shapiro et al., when discussing about loss of molecules as source of error in single-cell sequencing, it is written that:

Another source of error is losses, which can be severe. The detection limit of published protocols is $5$–$10$ molecules of mRNA.

I used to think that the detection limit of a protocol was the average maximum number of molecules detected across cells in a scRNA-seq experiment. However, by working on the dataset provided by The Tabula Muris Consortium et al. (pp) I noticed that RNA raw counts often spikes to more than 10 molecules.

What is the actual meaning of detection limit of a protocol in scRNA-seq?

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The detection limit refers to the ability to detect a given gene/transcript. In this case, they're saying that a given transcript requires 5-10 copies in order to be likely detected (in other words, the loss rate is 80-90%, which is directly related to a previous question of yours).

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  • $\begingroup$ Exactly, in that question I misunderstood the concept of detection limit. Now it's clear, thanks. $\endgroup$
    – gc5
    Jan 10, 2018 at 23:28

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