normalization.boxplot: Boxplot of gene expressions
In asael697/fdaRNA: RNA-Seq and Microarray Preprocessing

Description Usage Arguments Details Value Author(s) References Examples

View source: R/normalization.boxplot.R

Boxplot of the "log(ar+1)" transform of the data before and after the statistical functional depth based normalization. This is commonly carried out to show the adequacy of the procedure.

normalization.boxplot(
  ar,
  namesN = T,
  before = F,
  after = T,
  par.r = F,
  par.c = F,
  arg1 = "Before",
  arg2 = "After"
)

`ar`	Cell files from Affy micrarray experiment: a matrix where the columns are the sample elements, RNA-seq or microarray, and the rows the variables (the genes).
`namesN`	If TRUE, the labels of each RNA-seq's or microarray are substituted by a number corresponding to its position in data matrix. The default is TRUE.
`before`	If TRUE, the "log(ar+1)" transform of the data before the normalization step is plotted. The default is FALSE.
`after`	If TRUE, the "log(ar+1)" transform of the data after the normalization step is plotted. The default is TRUE.
`par.r`	If TRUE, and both "before" and "after" are also TRUE, the "before" and "after" boxplots are displayed in a row. The default is FALSE.
`par.c`	IIf TRUE, and both "before" and "after" are also TRUE, the "before" and "after" boxplots are displayed in a column. The default is FALSE.
`arg1`	Overall title for the boxplot before the normalization step. The default is Before.
`arg2`	Overall title for the boxplot after the normalization step. The default is After.

Boxplot of the "log(ar+1)" transform of the data before and after the normalization step. This is commonly carried out to show the adequacy of the procedure.

The boxplot of the "log( +1)" transform of the data before and/or after the normalization step.

A. Nieto and J. Cabrera

Nieto-Reyes A, Cabrera J. Statistical depth based normalization and outlier detection of gene expression data. Preprint.

## Computes the normalization of the RNA-seq's in the Airway dataset.
N = normalization(Airway)

## Displays in a row the boxplots of the "log(+1)" transform 
## of the data before and after normalization.

normalization.boxplot(Airway, before = TRUE, par.r = TRUE)