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 ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide https://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
