debaseline: Remove baseline from amplification curves (BETA)

In ewallace/tidyqpcr: Quantitative PCR Analysis with the Tidyverse

Remove baseline from amplification curves (BETA)

Description

Remove baseline from qPCR amplification curves by subtracting median of initial cycles.

Usage

debaseline(plateamp, maxcycle = 10)

Arguments

plateamp	data frame with plate amplification data, including variables well, cycle, fluor_raw (raw fluorescence value), and program_no. Assume program 2 for amplification curves from Roche Lightcycler format data.
maxcycle	maximum cycle value to use for baseline, before amplification.

Details

BETA function version because:

- assumes Roche Lightcycler format, we should ideally replace "program_no == 2" by something more generic?

- the rule-of thumb "baseline is median of initial 10 cycles" has not been tested robustly

Value

platemap with additional columns per well:

fluor_base	baseline /background value
fluor_signal	normalized fluorescence signal, i.e. fluor_raw - fluor_base

Examples

# create simple dataset of raw fluorescence
# with two samples over 15 cycles
raw_fluor_tibble <- tibble(sample_id = rep(c("S1", "S2"), each = 15),
                          target_id = "T1",
                          well_row = "A",
                          well_col = rep(c(1, 2), each = 15),
                          well = rep(c("A1", "A2"), each = 15),
                          cycle = rep(1:15,2),
                          fluor_raw = c(1:15, 6:20),
                          program_no = 2)

# remove base fluorescence from dataset
raw_fluor_tibble |>
    debaseline()
    

ewallace/tidyqpcr documentation built on June 5, 2024, 10:04 a.m.