<p>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 href="https://bioinformatics.stackexchange.com/questions/3126/how-to-compute-the-chance-of-failing-to-detect-a-gene-given-the-detection-limit">a previous question of yours</a>).</p>

CC BY-SA 3.0
2018-01-10T23:28:02.907Z
Exactly, in that question I misunderstood the concept of detection limit. Now it's clear, thanks.
gc5
CC BY-SA 3.0
2018-01-10T23:23:42.420Z
2018-01-10T23:23:42.420Z
Devon Ryan
<p>In <a href="https://www.nature.com/articles/nrg3542" rel="nofollow noreferrer">Shapiro et al.</a>, when discussing about loss of molecules as source of error in single-cell sequencing, it is written that:</p>

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

<p>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 <a href="https://www.biorxiv.org/content/early/2017/12/20/237446" rel="nofollow noreferrer">The Tabula Muris Consortium et al. (pp)</a> I noticed that RNA raw counts often spikes to more than 10 molecules.</p>

<p>What is the actual meaning of detection limit of a protocol in scRNA-seq?</p>

<scrnaseq>
What is the detection limit of protocol in scRNA-seq
# What is the detection limit of protocol in scRNA-seq

(Asked by: username_0 on 2018-01-10)

In [Shapiro et al.](https://www.nature.com/articles/nrg3542), 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)](https://www.biorxiv.org/content/early/2017/12/20/237446) 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?

**Tags:** scrnaseq

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## 1 answers

### Answer by username_1 on 2018-01-10. Score: 1 | Accepted answer

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](https://bioinformatics.stackexchange.com/questions/3126/how-to-compute-the-chance-of-failing-to-detect-a-gene-given-the-detection-limit)).

> **Comments:**
> **username_0**: Exactly, in that question I misunderstood the concept of detection limit. Now it's clear, thanks.  

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