estimateMAValues: Estimation of the M and A Values

In adele/omicsMA: Variance-Preserving Estimation and Normalization of M-A Values

Estimation of the M and A Values

Description

Estimates the intensity values M and A, considering p spots/genes and n microarray slides, by using the conventional method \insertCiteyang2002comparisonomicsMA or the one that takes into account pixel-level variability \insertCiteribeiro2019omicsMAomicsMA.

Usage

estimateMAValues(R.mean, G.mean, R.var, G.var, RG.cov, R.bckg, G.bckg,
  estimator = "second-order", bgcorr = "normexp", offset = 50,
  putaway.perc = 0.05, array.ids = NULL, gene.ids = NULL)

Arguments

R.mean	A p x n matrix of mean values for the red (test) foreground intensities.
G.mean	A p x n matrix of mean values for the green (reference) foreground intensities.
R.var	A p x n matrix of variances of the red foreground intensities.
G.var	A p x n matrix of variances of the green foreground intensities.
RG.cov	A p x n matrix of covariances between the green and red foreground intensities.
R.bckg	A p x n matrix of mean values of the red background intensities.
G.bckg	A p x n matrix of mean values of the green background intensities.
estimator	A character string indicating the estimation method. The options are 'conventional' and 'second-order'. If estimator is set as 'second-order', then an estimator that takes into account pixel-level variability is used.
bgcorr	A character string indicating the background correction method. The options are 'none' and 'normexp'.
offset	A numeric parameter for the normexp background correction.
putaway.perc	A scalar between 0 and 100 indicating percentage of genes expressions. with high variance to be discarded. Default is 0.05.
array.ids	A character vector with identifiers of the arrays.
gene.ids	A character vector with identifiers of the genes.

Value

A limma's MAlist object with the M and A values

References

\insertAllCited

Examples

data(metaplasia)
MA <- estimateMAValues(metaplasia$R.mean, metaplasia$G.mean,
                       metaplasia$R.var, metaplasia$G.var, metaplasia$RG.cov,
                       metaplasia$R.bckg, metaplasia$G.bckg,
                       array.ids=metaplasia$array.ids, gene.ids=metaplasia$gene.ids)

adele/omicsMA documentation built on July 4, 2025, 3:49 a.m.