Type: Package
Title: Biomarker Data Set by Vermeulen et al. (2009)
Version: 0.1.2
Description: The biomarker data set by Vermeulen et al. (2009) <doi:10.1016/S1470-2045(09)70154-8> is provided. The data source, however, is by Ruijter et al. (2013) <doi:10.1016/j.ymeth.2012.08.011>. The original data set may be downloaded from https://medischebiologie.nl/wp-content/uploads/2019/02/qpcrdatamethods.zip. This data set is for a real-time quantitative polymerase chain reaction (PCR) experiment that comprises the raw fluorescence data of 24,576 amplification curves. This data set comprises 59 genes of interest and 5 reference genes. Each gene was assessed on 366 neuroblastoma complementary DNA (cDNA) samples and on 18 standard dilution series samples (10-fold 5-point dilution series x 3 replicates + no template controls (NTC) x 3 replicates).
License: CC BY 4.0
Encoding: UTF-8
RoxygenNote: 7.3.1
Depends: R (≥ 2.10)
Imports: memoise
Suggests: dplyr, ggplot2, rmarkdown, spelling, testthat (≥ 3.0.0), tibble
Language: en-US
URL: https://github.com/ramiromagno/vermeulen, https://rmagno.eu/vermeulen/
BugReports: https://github.com/ramiromagno/vermeulen/issues
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2024-04-22 21:30:34 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 22:40:03 UTC

vermeulen: Biomarker Data Set by Vermeulen et al. (2009)

Description

The biomarker data set by Vermeulen et al. (2009) doi:10.1016/S1470-2045(09)70154-8 is provided. The data source, however, is by Ruijter et al. (2013) doi:10.1016/j.ymeth.2012.08.011. The original data set may be downloaded from https://medischebiologie.nl/wp-content/uploads/2019/02/qpcrdatamethods.zip. This data set is for a real-time quantitative polymerase chain reaction (PCR) experiment that comprises the raw fluorescence data of 24,576 amplification curves. This data set comprises 59 genes of interest and 5 reference genes. Each gene was assessed on 366 neuroblastoma complementary DNA (cDNA) samples and on 18 standard dilution series samples (10-fold 5-point dilution series x 3 replicates + no template controls (NTC) x 3 replicates).

Author(s)

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

Other contributors:

See Also

Useful links:

Import the Biomarker data set

Description

This function retrieves the Biomarker data set, a data set containing raw fluorescence amplification data: 24,576 amplification curves, of 50 cycles each.

Usage

get_biomarker_dataset()

Details

Data was gathered from Ruijter et al. (2013), doi:10.1016/j.ymeth.2012.08.011 but original source is by Vermeulen et al. (2009), doi:10.1016/S1470-2045(09)70154-8. The tidy version of the data is kept at the repository of the source of {vermeulen} package. This function fetches such data and thus requires internet connection. It takes a few seconds to run.

The Biomarker data set comprises a set of 59 targets previously identified as a 59-mRNA gene expression signature, that has been developed and validated for improved outcome prediction of children with neuroblastoma. In short, 59 biomarkers and 5 reference genes were measured in 8 µl reactions in a 384-well plate using the LightCycler480 SYBR Green Master (Roche) in a sample maximization experiment design. The 59 genes were carefully selected as being previously reported as prognostic genes in neuroblastoma in at least two independent studies. Each plate contained 366 cDNA samples (n = 1) from primary tumor biopsies, a 5-point 10-fold serial dilution series based on an external oligonucleotide standard (n = 3, from 150,000 to 15 copies), and a no template control (NTC, n = 3). Raw (baseline uncorrected) fluorescent data were exported from the LightCycler480 instrument software.

Value

A data frame with 24,576 amplification curves, of 50 cycles each:

plate

Plate identifier. Because one plate was used per gene, the name of the plate is the same as the values in target.

well

Well identifier.

dye

In all reactions the SYBR Green I master mix (Roche) was used, so the value is always "SYBR".

target

Target identifier, in almost all cases the name of a gene.

target_type

Target type: either target of interest ("toi") or reference target ("ref").

sample

Sample identifier.

sample_type

Sample type.

copies

Standard copy number.

dilution

Dilution factor. Higher number means greater dilution.

cycle

PCR cycle.

fluor

Raw fluorescence values.

Source

Examples


# Takes ~ 10-30 sec
head(get_biomarker_dataset())