dpcR (version 0.1.2-1)

pds: Plasmid dilution series results

Description

These are the results data from the pds_raw data as calculated by the BioRad QX100 Droplet Digital PCR System.

Setup: Duplex assay with constant amount of genomic DNA and six 10-fold dilutions of plasmid DNA with 4 replicates, ranging theoretically from ~ 10^4 to 10^-1 copies/ micro L plus 4 replicates without plasmid DNA. Included are No-gDNA-control and No-template-control, 2 replicates each.

Annotation: FX.Y (X = dilution number, Y = replicate number). Hardware: Bio-Rad QX100 Droplet digital PCR system Details: Genomic DNA isolated from Pseudomonas putida KT2440. Plasmid is pCOM10-StyA::EGFP StyB [Jahn et al., 2013, Curr Opin Biotechnol, Vol. 24 (1): 79-87]. Template DNA was heat treated at 95 degree Celsius for 5 min prior to PCR. Channel 1, primers for genomic DNA marker ileS, Taqman probes (FAM labelled). Channel 2, primers for plasmid DNA marker styA, Taqman probes (HEX labelled).

Usage

data(pds)

source

Michael Jahn Flow cytometry group / Environmental microbiology Helmholtz Centre for Environmental Research - UFZ Permoserstrasse 15 / 04318 Leipzig / Germany phone [phone] michael.jahn [at] ufz.de / www.ufz.de

References

Jahn et al., 2013, Curr Opin Biotechnol, Vol. 24 (1): 79-87

Examples

# Loading libraries
library(lattice)
library(latticeExtra)
library(gplots)
library(Hmisc)
library(memisc)

dat <- pds
dat$Dilution <- rep(c(rep(c(10^(4:-1),0), each = 4), 
		    "NGC", "NGC", "NTC", "NTC"), 2)

print(xyplot(Concentration ~ factor(Dilution, levels=Dilution), dat, 
      groups = Assay, ewidth = 0.08, ylim = c(10^-1.5, 10^4.5),
      ylab = "Concentration cp / micro L", xlab = "Theoretical plasmid 
	      concentration [cp/micro L]", strip = FALSE,
    scales = list(y = list(log = 10), alternating = FALSE),
    panel = function(x, y, groups = groups, ...) {
        panel.rect(7.5,-2, 10,5, col = grey(0.9), border = NA)
        panel.grid(h = -1,v = -1, col = grey(0.8), lty = 2)
        panel.xyplot(x, y, groups = groups, col = grey(0.6), ...)
        panel.key(c("IleS", "StyA"), corner = c(0.95,0.95))
        means <- tapply(y, list(x, groups), function(x) mean(x, na.rm = TRUE))
        stdev <- tapply(y, list(x, groups), function(x) sd(x, na.rm = TRUE))
        panel.errbars(1:9 + 0.25, y = cbind(means[, 1], 
		      means[, 1]-stdev[, 1], means[, 1] + stdev[, 1]), 
		      make.grid = "none", pch = 1,...)
        panel.errbars(1:9 + 0.25, y = cbind(means[, 2], 
		      means[, 2] - stdev[, 2], means[, 2] + stdev[, 2]), 
		      make.grid = "none", pch = 3, ...)
        panel.abline(a = c(5,-1), lty = 2, col = 2)
    }
  )
)