VIMiQ5_685

<p>Data set of an amplification reaction using the Bio-Rad iQ5 thermo cycler. The 
samples of Vimentin were amplified in the iQ5 as replicates according to 
Roediger et al. (2013). The quantification was performed during the elongation 
step (68.5 degrees Celsius).</p>

datasets

Elongation

A collection of functions to pre-process amplification curve data from polymerase chain reaction (PCR) or isothermal amplification reactions. Contains functions to normalize and baseline amplification curves, to detect both the start and end of an amplification reaction, several smoothers (e.g., LOWESS, moving average, cubic splines, Savitzky-Golay), a function to detect false positive amplification reactions and a function to determine the amplification efficiency. Quantification point (Cq) methods include the first (FDM) and second approximate derivative maximum (SDM) methods (calculated by a 5-point-stencil) and the cycle threshold method. Data sets of experimental nucleic acid amplification systems ('VideoScan HCU', capillary convective PCR (ccPCR)) and commercial systems are included. Amplification curves were generated by helicase dependent amplification (HDA), ccPCR or PCR. As detection system intercalating dyes (EvaGreen, SYBR Green) and hydrolysis probes (TaqMan) were used. For more information see: Roediger et al. (2015) <doi:10.1093/bioinformatics/btv205>.

Stefan Roediger

chipPCR

Toolkit of Helper Functions to Pre-Process Amplification Data

Michal Burdukiewicz

Konstantin A. Blagodatskikh

Andrej-Nikolai Spiess

VIMiQ5_685 function

<p>A data frame with 40 observations on the following 97 variables. The first 
  column ("Cycles") contains the number of cycles and consecutive columns 
  contain the replicates ("A01" to "H12").</p>

Format

Amplification Reaction Using the Bio-Rad iQ5 — VIMiQ5_685

Amplification Reaction Using the Bio-Rad iQ5

VIMiQ5_685: Amplification Reaction Using the Bio-Rad iQ5

Description

Usage

Arguments

Format

References

Examples