bg_correct — bg_correct • protGear
Description: A generic function to perform background correction.

# bg_correct

Source: `R/read_files_functions.R`
`bg_correct.Rd`

A generic function to perform background correction.

    bg_correct(iden, Data1, genepix_vars, method = "subtract_local")

## Arguments

iden

  A character indicating the name of the object to be used under Data1

Data1

  A data frame with sample identifiers merged with micro array data.

genepix_vars

  A list of specific definitions of the experiment design. See `array_vars`.

method

  a description of the background correction to be used. Possible values are `"none","subtract_local", "subtract_global","movingmin_bg","minimum_half","edwards" or "normexp"`. The default is `"subtract_local"`.

## Value

A data frame with background corrected data

## Details

Background correction

The function implements background correction methods developed by `backgroundCorrect`. But the `minimum_half and movingmin_bg` uses the block of the protein array as the grid. If method="movingmin_bg" the minimum background value within a block is subtracted. If method="minimum_half" then any intensity which is negative after background subtraction is reset to be equal to half the minimum positive value in a block. If method="movingmin_value" then any intensity which is negative after background subtraction is reset to the minimum positive value in a block. For `edwards` we implement a similar algorithm with `limma::backgroundCorrect(method="edwards")` and for `'normexp'` we use the saddle-point approximation to maximum likelihood, `backgroundCorrect` for more details.