effcalc: Analysis of the amplification efficiency

Description Usage Arguments Value Author(s) References See Also

View source: R/effcalc.R

Description

effcalc calculates the amplification efficiency of a dilution.

Usage

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## 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)        

Arguments

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.

Value

an object of the class eff.

Author(s)

Stefan Roediger

References

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.

See Also

eff

plot.eff


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