Hello,
I would like to analyze quantitative PCR (qPCR) data using R rather
than proprietary softwares.
I can see there are several packages out there, but mostly they
perform relative quantification, while none provide a quantitative
cycle (Cq), or crossing over cycle.
Is there a package that can provide a Cq for a given threshold level?
Or is it possible to determine the value with regression?
I can fit a model on qPCR data using for instance the package qpcR
(https://cran.r-project.org/web/packages/qpcR/index.html):
```
val = c(120.64, 66.14, 34.87, 27.11, 8.87, -5.8,
4.52, -7.16, -17.39,
-14.29, -20.26, -14.99, -21.05, -20.64, -8.03,
-21.56, -1.28, 15.01,
75.26, 191.76, 455.09, 985.96, 1825.59,
2908.08, 3993.18, 5059.94,
6071.93, 6986.32, 7796.01, 8502.25, 9111.46,
9638.01, 10077.19,
10452.02, 10751.81, 11017.49, 11240.37, 11427.47,
11570.07, 11684.96,
11781.77, 11863.35, 11927.44, 11980.81, 12021.88,
12058.35, 12100.63,
12133.57, 12148.89, 12137.09)
x <- data.frame(Cycles = 1:35, val)
library(qpcR)
fit <- pcrfit(data=x, # selected data
cyc=1, fluo=2) # columns for cycles and fluorescence
summary(fit)
```
The package allows the determination of a take-over point, but this is
the cycle where the data start moving into the exponential phase:
```
takeoff(fit, pval = 0.05, nsig = 3)
```
However, this level is too low; the Cq would probably be way higher on
the y-axis, and there are instances where I would like to use a
pre-fixed threshold value.
How can I determine a Cq with R?
Thank you
--
Best regards,
Luigi