normLoess: Normalization by loess method

In eg-r/sights: Statistics and dIagnostic Graphs for HTS

Normalization by loess method

Description

Apply loess normalization to data

Usage

normLoess(dataMatrix, plateRows, plateCols, dataRows = NULL,
  dataCols = NULL)

Arguments

dataMatrix	Data frame or numeric matrix. Columns are plates, and rows are plate wells.
plateRows, plateCols	Number of rows/columns in plate.
dataRows, dataCols	Optional integer vector. Indicate which row/column numbers from the dataMatrix should be normalized. If NULL then all rows/columns from the dataMatrix are used.

Details

Loess normalization adjusts each well by the fitted row and column values generated by calculating the loess curve for each row and column.

Value

Numeric matrix of normalized data in the same format as dataMatrix

Note

For information on how to arrange your dataset for dataMatrix, please see (ex_dataMatrix)

References

Baryshnikova et al. (2010). Quantitative analysis of fitness and genetic interactions in yeast on a genome scale. Nature Methods, 7(12), 1017-1024.

See Also

Other normalization methods: normMedFil, normRobZ, normR, normSPAWN, normZ

Examples

## load dataset
data(ex_dataMatrix)

## apply Loess method
ex_normMatrix <- normLoess(dataMatrix = ex_dataMatrix, dataCols = 5:10,
plateRows = 8, plateCols = 10)

eg-r/sights documentation built on Jan. 28, 2023, 12:17 a.m.