qubitr: qubitr: Analyse Results from the Clariostar Qubit Assay

In TomHarrop/qubitr: Analyse Results from the Clariostar Qubit Assay

Description

qubitr: Analyse Results from the Clariostar Qubit Assay

Example analysis

library(data.table)
library(qubitr)

load the raw data. You'll need columns called `plate_row`, `plate_col` and
`raw_fl` for the analysis. `content` helps you find the blank and standard
wells.
rename <- c("plate_row",
            "plate_col",
            "content",
            "raw_fl")

# this command will be different for different input files, especially the
# `skip` argument.
raw_data <- fread("my_clariostar_data.csv",
                  skip = 11,
                  select = c(1:4),
                  col.names = rename)

# make sure it looks OK
head(raw_data)

# where are the standards?
raw_data[grep("^Standard", content)]

# where are the blanks?
raw_data[grep("^Blank", content)]

# add volumes (**SIDE EFFECTS**: this modifies `raw_data`)
AddVolumes(raw_data, "A1", "D5", 1, 50)
AddVolumes(raw_data, "A6", "H6", 1, 50)
AddVolumes(raw_data, "A7", "H11", 10, 800)
AddVolumes(raw_data, "E5", "H5", 10, 800)

# subtract background
background_subtracted <- SubtractBackground(raw_data, c("A12", "B12"))

# run the linear model
standard_wells <- data.table(well = paste0(LETTERS[3:8], 12),
                             amount = c(rep(10, 3), rep(100, 3)))
calculated_amounts <- CalculateAmounts(background_subtracted, standard_wells)

# get the results
final_results <- ExtractResults(calculated_amounts)

head(final_results)

TomHarrop/qubitr documentation built on May 14, 2019, 9:38 a.m.