addnorm {flowTime} | R Documentation

## Normalize fluorescence

### Description

Produces a normalized fluorescence column 'normed'. Expects the 'FL1.A_bs' column to exist or a column to be specified. Has three different methods, version 1 and version 2, described in the script

### Usage

    addnorm(
      frame,
      factor_in = c("strain", "treatment"),
      method = 1,
      column = "FL3.Amean_bs"
    )

### Arguments

`frame` | `data frame` of summary statistics to be normalized
`factor_in` | `character vector` containing the varibles to split the data frame by
`method` | which normalization method to use, 1, 2 or 3.
`column` | `character` the column to apply the normalization to

### Details

Method 1, the default normalization method, takes the highest point in each dataset grouped by 'factor_in' and normalizes all values in the group by this point. This method is default because it works regardless of whether the data is a time series. Method 2 finds the mean value of all time points with time values less than 0 for each group and normalizes each group by this respective value. Requires a time series with negative time values to work. Method 3 fits a linear model to the pre-zero time points for each groups, infers the y-intercept, and normalizes using this intercept. Method 3 also requires a time series with negative time values to work.

### Value

`data frame` containing the additional normalized variable

### Examples

    dat <- read.flowSet(path=system.file("extdata", "tc_example",
    package = "flowTime"), alter.names = TRUE)
    annotation <- read.csv(system.file("extdata", "tc_example.csv",
    package = "flowTime"))
    adat <- annotateFlowSet(dat, annotation)
    loadGates(gatesFile = 'C6Gates')
    dat_sum <- summarizeFlow(adat, ploidy = "diploid", only = "singlets",
    channel = "FL1.A")
    dat_sum <- addnorm(dat_sum, c("strain", "treatment"), method = 1,
    column = "FL1.Amean")

[Package flowTime version 1.16.1 Index]