Type: Package
Title: Real-Time PCR Data Sets by Rutledge et al. (2004)
Version: 0.1.1
Description: Real-time quantitative polymerase chain reaction (qPCR) data by Rutledge et al. (2004) <doi:10.1093/nar/gnh177> in tidy format. The data comprises a six-point, ten-fold dilution series, repeated in five independent runs, for two different amplicons. In each run, each standard concentration is replicated four times. For the original raw data file see the Supplementary Data section: https://academic.oup.com/nar/article/32/22/e178/2375678#supplementary-data.
License: CC BY 4.0
Encoding: UTF-8
LazyData: true
Depends: R (≥ 2.10)
RoxygenNote: 7.3.1
Imports: tibble
URL: https://github.com/ramiromagno/rutledge, https://rmagno.eu/rutledge/
BugReports: https://github.com/ramiromagno/rutledge/issues
NeedsCompilation: no
Packaged: 2024-04-22 21:32:58 UTC; rmagno
Author: Ramiro Magno ORCID iD [aut, cre], Pattern Institute [cph, fnd]
Maintainer: Ramiro Magno <rmagno@pattern.institute>
Repository: CRAN
Date/Publication: 2024-04-22 22:40:10 UTC

rutledge: Real-Time PCR Data Sets by Rutledge et al. (2004)

Description

Real-time quantitative polymerase chain reaction (qPCR) data by Rutledge et al. (2004) doi:10.1093/nar/gnh177 in tidy format. The data comprises a six-point, ten-fold dilution series, repeated in five independent runs, for two different amplicons. In each run, each standard concentration is replicated four times. For the original raw data file see the Supplementary Data section: https://academic.oup.com/nar/article/32/22/e178/2375678#supplementary-data.

Author(s)

Maintainer: Ramiro Magno rmagno@pattern.institute (ORCID)

Other contributors:

See Also

Useful links:

qPCR data set by Rutledge et al. (2004)

Description

Each data set comprises a six-point, ten-fold dilution series, repeated in five independent runs, for two different amplicons: K1/K2, 102 bp, and K3/K2, 218 bp. Fluorescence readings were exported after background subtraction via baseline averaging of the 5 cycles immediately preceding the cycles in which fluorescence was first detected. Please read the Materials and Methods section of Rutledge et al. (2004) for more details.

Format

A tibble with 10,800 rows and 10 variables:

plate

Plate identifier. Because one plate (run) was used per dilution series, plate values are simply numbered 1 thru 5.

well

Well identifier. Values are always NA (not available). This variable is kept nevertheless to be coherent with other data sets from other similar R data packages.

dye

The type of dye used. In this data set the values are always "SYBR", meaning SYBR Green I master mix (Roche).

target

Target identifier: the amplicon used, K1/K2 or K3/K2.

sample_type

Sample type (all curves are standards, i.e. "std").

replicate

Replicate identifier: 1 thru 4.

copies

Standard copy number.

dilution

Dilution factor. Higher number means greater dilution.

cycle

PCR cycle.

fluor

Raw fluorescence values.

Source

doi:10.1093/nar/gnh177

Examples

rutledge