effcalc: Analysis of the amplification efficiency
In chipPCR: Toolkit of Helper Functions to Pre-Process Amplification Data

Description Usage Arguments Value Author(s) References See Also

effcalc calculates the amplification efficiency of a dilution.

## S4 method for signature 'numeric,numeric'
effcalc(x, y, logx = TRUE, RSD = FALSE, rob = FALSE,
                                    level = 0.95)
## S4 method for signature 'matrix,missing'
effcalc(x, y, logx = TRUE, RSD = FALSE, rob = FALSE,
                                   level = 0.95)
## S4 method for signature 'matrix,missing'
effcalc(x, y, logx = TRUE, RSD = FALSE, rob = FALSE,
                                   level = 0.95)

`x`	is the column of a data frame for the concentration (dilution).
`y`	are multiple columns of Cq values from a `data.frame` (e.g., [, c(1:n)]).
`logx`	is a logical parameter used to convert the concentration into a decadic logarithm.
`RSD`	Setting the option `RSD = TRUE` shows the relative standard deviation (RSD) in percent.
`rob`	Using the option `rob` as TRUE the median and the median absolute deviation (MAD) is plotted instead of the mean and standard deviation.
`level`	Tolerance/confidence level.

an object of the class eff.

Stefan Roediger

A Highly Versatile Microscope Imaging Technology Platform for the Multiplex Real-Time Detection of Biomolecules and Autoimmune Antibodies. S. Roediger, P. Schierack, A. Boehm, J. Nitschke, I. Berger, U. Froemmel, C. Schmidt, M. Ruhland, I. Schimke, D. Roggenbuck, W. Lehmann and C. Schroeder. Advances in Biochemical Bioengineering/Biotechnology. 133:33–74, 2013.

S. Mehra and W.-S. Hu. A kinetic model of quantitative real-time polymerase chain reaction. Biotechnology and bioengineering, 91(7):848–860, Sept. 2005. ISSN 0006-3592. doi: 10.1002/bit.20555. PMID: 15986490.

M. Guescini, D. Sisti, M. B. Rocchi, L. Stocchi, and V. Stocchi. A new real-time PCR method to overcome significant quantitative inaccuracy due to slight amplification inhibition. BMC Bioinformatics, 9(1):326, July 2008. ISSN 1471-2105. doi: 10.1186/1471-2105-9-326. PMID: 18667053.

A. Tichopad, M. Dilger, G. Schwarz, and M. W. Pfaffl. Standardized determination of real-time PCR efficiency from a single reaction set-up. Nucleic Acids Research, 31(20):e122, Oct. 2003. ISSN 1362-4962. PMID: 14530455 PMCID: PMC219490.

A. Staalberg, P. Aman, B. Ridell, P. Mostad, and M. Kubista. Quantitative real-time PCR method for detection of b-lymphocyte monoclonality by comparison of kappa and lambda immunoglobulin light chain expression. Clinical Chemistry, 49(1):51–59, Jan. 2003. ISSN 0009-9147. PMID: 12507960.

W. Liu and D. A. Saint. A new quantitative method of real time reverse transcription polymerase chain reaction assay based on simulation of polymerase chain reaction kinetics. Analytical Biochemistry, 302(1):52–59, Mar. 2002. ISSN 0003-2697. doi: 10.1006/abio.2001.5530. PMID: 11846375.

eff

plot.eff

chipPCR documentation built on March 5, 2021, 9:06 a.m.