# assessQuality: Quality assessment for cleaning procedures. In RUVcorr: Removal of unwanted variation for gene-gene correlations and related analysis

## Description

assessQuality allows to assess the quality of cleaning procedures in the context of correlations when the true underlying correlation structure is known.

## Usage

 1 2 3 4 5 6 assessQuality( est, true, index = "all", methods = c("all", "fnorm", "wrong.sign") ) 

## Arguments

 est A matrix of estimated gene expression values. true A matrix of true correlations. index A vector of indices of genes to be included in the assessment; if index="all" all genes are considered. methods The method used for quality assessment; if method="fnorm" the squared Frobenius norm is used; if method="wrong.sign" the percentage of wrongly estimated signs is calculated if method="all" both are calculated.

## Details

The squared Frobenius norm used for assessQuality has the following structure

F=\frac{\|E-T\|^2}{s}

Here, the parameter E and the parameter T denote the lower triangles of the estimated and true Fisher transformed correlation matrices, respectively. The parameter s denotes the number of elements in E and T.

## Value

assessQuality returns a vector of the requested quality assessments.

## Author(s)

 1 2 3 4 Y<-simulateGEdata(500, 500, 10, 2, 5, g=NULL, Sigma.eps=0.1, 250, 100, intercept=FALSE, check.input=FALSE) assessQuality(Y$Y, Y$Sigma, index=1:100, methods="wrong.sign") assessQuality(Y$Y, Y$Sigma, index=1:100, method="fnorm")