get_biomarker_dataset: Import the Biomarker data set

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

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), \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.ymeth.2012.08.011")} but original source is by Vermeulen et al. (2009), \Sexpr[results=rd]{tools:::Rd_expr_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

• https://medischebiologie.nl/wp-content/uploads/2019/02/qpcrdatamethods.zip

• https://github.com/ramiromagno/vermeulen/tree/main/data-raw

Examples

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

vermeulen documentation built on May 29, 2024, 12:06 p.m.