dpcR (version 0.3)

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.

Format

A data frame with 64 observations on the following 44 variables.

Well

a factor with levels A01 to H04

ExptType

a factor with levels Absolute Quantification

Experiment

a factor with levels ABS

Sample

a factor with levels B B + P 10^2 gDNA gDNA + P 10^0 gDNA + P 10^1 gDNA + P 10^-1 gDNA + P 10^2 gDNA + P 10^3 gDNA + P 10^4

TypeAssay

a factor with levels Ch1NTC Ch1Unknown Ch2NTC Ch2Unknown

Assay

a factor with levels ileS styA

Status

a factor with levels Manual

Concentration

a numeric vector

TotalConfMax

a logical vector

TotalConfMin

a logical vector

PoissonConfMax

a numeric vector

PoissonConfMin

a numeric vector

Positives

a numeric vector

Negatives

a numeric vector

Ch1.Ch2.

a numeric vector

Ch1.Ch2..1

a numeric vector

Ch1.Ch2..2

a numeric vector

Ch1.Ch2..3

a numeric vector

Linkage

a numeric vector

AcceptedDroplets

a numeric vector

CNV

a logical vector

TotalCNVMax

a logical vector

TotalCNVMin

a logical vector

PoissonCNVMax

a logical vector

PoissonCNVMin

a logical vector

ReferenceCopies

a logical vector

UnknownCopies

a logical vector

Ratio

a numeric vector

TotalRatioMax

a logical vector

TotalRatioMin

a logical vector

PoissonRatioMax

a numeric vector

PoissonRatioMin

a numeric vector

FractionalAbundance

a numeric vector

TotalFractionalAbundanceMax

a logical vector

TotalFractionalAbundanceMin

a logical vector

PoissonFractionalAbundanceMax

a numeric vector

PoissonFractionalAbundanceMin

a numeric vector

ReferenceAssayNumber

a numeric vector

TargetAssayNumber

a numeric vector

MeanAmplitudeofPositives

a numeric vector

MeanAmplitudeofNegatives

a numeric vector

MeanAmplitudeTotal

a numeric vector

ExperimentComments

a logical vector

MergedWells

a logical vector

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

Details

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).

References

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

Examples

summary(extract_dpcr(read_QX100(pds), 1L:10))