Biology Forums - Study Force

A certain tissue shows no activity found before the set cycle baseline. I need to keep these values and representing them as 0 is a misrepresentation of what actually occurred.
 
There is no error in the way the experiment was carried out there just isn't any activity before the baseline for this tissue.

It would be so helpful if someone could tell me an alternative way to note Ct values which explain what's happening.

Thank You

Hi!

The attachment might help :)

Would there be a way to represent the value numerically when it's an unknown cycle number.

In a very simple sense, if you subtract Ct (reference) gene from Ct (Gene of interest).

1) No change in ∆Ct means the level of gene of interest is similar to reference gene
2) +ve ∆Ct means gene is expressed at lower level than reference gene
3) -ve ∆Ct means gene is expressed at higher level than reference gene
4) Undetermined Ct indicates that the instrument could not detect your gene under the assay conditions used... and there can be many reasons for that.

Disagree ^^

The Ct value is proportional to -log(N), where N is the initial number of target molecules. The higher N, the lower is the Ct. As N goes to zero, -log(N) goes to infinity. Thus, the Ct value of a sample with zero target molecules would actually be infinity: the amplification curve will never rise (due to the specific amplification of the target sequence) and will thus never cross a threshold level. So theoretically you can substitute "Undetermined" by "Infinity". Practically, you can not know if target molecules were present and the actually performed number of amplification cycles was just not sufficient to reach the threshold, or if the reaction/detection just did not work. Therefore "Undetermined" is the better word here.

A negative ∆Ct just means that a higher Ct value was subtracted from a lower Ct value. That's all. There is no meaningful interpretation; this is just a mathematical fact.

Note: Since Ct ~ -log(N), ∆Ct = Ct[A]-Ct[B] ~ (-log(N[A]))-(-log(N[B])) = log(N[B])-log(N[A]) = log(N[B]/N[A]). The ∆Ct is proportional to a log-ratio of initial copy numbers. One of the genes (A or B) is typically used as "loading control" (reference gene). If ∆Cts are determined for the same genes but under different conditions, the proportionality factors between conditions are still unknown but similar, so the ∆Cts can be compared over conditions.