Gallery - Example 5

Below is the R code to reproduce the example:

Hide output

library(DECIPHER)
> 
> probes <- DNAStringSet(c("AAGGTCGGCCGCTACAAGGT",
+    "GATGTCGTCGGTCTCGAC"))
> targets <- reverseComplement(probes)
> 
> FAs <- 0:70 # % formamide
> eff <- matrix(NA,
+    nrow=length(FAs),
+    ncol=length(probes))
> 
> for (i in seq_along(FAs))
+    eff[i,] <- CalculateEfficiencyFISH(probes,
+       targets,
+       46, # temp
+       250e-9, # [Po]
+       1, # [Na+]
+       FAs[i])[, "HybEff"]
> 
> matplot(FAs,
+    eff,
+    type="l",
+    ylab="Hybridization Efficiency",
+    xlab="Formamide Concentration (% v/v)",
+    col=3:4)
> legend("topright",
+    paste("Probe",
+       1:2),
+    lty=1:2,
+    col=3:4)