How would I do to set threshold with CHAI OPENQPCR?


#1

Dear Sir/Madam
I need some helps concerning the setting of threshold!
In CHAI OPENQPCR, the definition of threshold setting is “The threshold which the first/second derivative of the curve must exceed for a Cq to be called”.
Is the “derivative” a mathematic noun?
How do I know what numbers should I type in and how to calculate it for adjusting the threshold?
Thank you very much


#2

Hi Joseph! @super90579

Great questions!

Yes, the derivative is a mathematic noun. The 1st derivative of a certain point on a curve is the slope of that point (i.e. the slope of the line tangent to the curve at that point) whereas the 2nd derivative of a curve is the 1st derivative of the 1st derivate of the curve.

So the numbers to type in are dependent on your curve shape. Are you getting a Cq callout that shouldn’t be there or are you not getting an expected Cq callout?

If the latter - where you’re not getting a Cq callout - it’s likely that the curve slope(s) are not very steep. If that is the case, it’s best to adjust the min 1st and min 2nd derivatives (and possibly baseline cycles) to obtain the appropriate Cq callout. You will need to lower the default value for both min. 1st and min 2nd derivatives. As for baseline cycles, use values from the region of the curve that is flat and before any sort of signal or exponential amplification.

Cheers,
Lily


#3

Dear Lily
Thanks for your reply.
My question is that I cannot get an expected Cq callout.
So I need to test the numbers of 1st and min 2nd derivatives randomly with right direction for getting the Cq callout which I expected?
If I just only lower the value of 1st derivatives and don’t adjust the value of 2nd derivatives or in contrast. how the Cq callout will be changed?
I’m not very understand how to adjust the Cq callout with the derivative way.
Thanks for your assistance!


#4

Hi Joseph,

If you’d like, I’m happy to take a look at your curves and adjust your amp settings to find the values that are suitable for this experiment - I’ll just need your database. Feel free to send that over to support@chaibio.com.

Typically, adjusting the min 1st and min 2nd derivatives are dependent on the data. Sometimes, you will need to adjust both derivatives to obtain a Cq output. Currently, it’d be best to test the different values given the specs I previously provided.

After some user feedback, we understand this is a slightly complicated process so we’ll be displaying derivatives for each cycle in the UI with our upcoming software release. This should make it very easy for users to input the appropriate derivative values if amp settings adjustments need to be made.

Let me know if you have any further questions!

Cheers,
Lily