flu_norm: Normalise fluorescence against negative well autofluorescence
In ec363/fpcountr: Fluorescent Protein Calibration For Plate Readers

flu_norm

R Documentation

Normalise fluorescence against negative well autofluorescence

Description

Used by process_plate function for fluorescence normalisation. Remains virtually unchanged from flopr::flu_norm, except that af_model can be set to NULL to normalise to blank wells instead, and files are saved to a specified outfolder.

Usage

flu_norm(
  pr_data,
  neg_well,
  blank_well,
  flu_name,
  af_model,
  data_csv,
  timecourse,
  outfolder
)

Arguments

`pr_data`	a long data.frame containing you plate reader data with OD normalised
`neg_well`	the well coordinates of a non-fluorescent control
`blank_well`	the well coordinates of a media blank
`flu_name`	the column name of the fluorescence channel to normalise
`af_model`	model used to fit negative control autofluorescence. For now these include "polynomial", "inverse_poly", "exponential", "spline" or "loess". If set to NULL, no model is used, and fluorescence is normalised akin to OD: by subtracting the value for the blanks.
`data_csv`	path to the original data. Used for saving normalisation curve plots.
`timecourse`	logical. Is the data timecourse/kinetic data and does it include a variable called 'time'?
`outfolder`	path to folder where output files should be saved. Defaults to current working directory.