vm.analysis.paired.step.1 {varmixt}R Documentation

First step of analysis in paired data case

Description

Function to do the first step of analysis in paired data case

Usage

vm.analysis.paired.step.1(geneId, ratio, meanint = NULL, gene.anot = NULL, badqual = NULL, qualtol = NULL, center = TRUE, loess.cor = FALSE, min.rep = 2)

Arguments

geneId a vector of the vector of gene names
ratio a matrix of the normalized log-ratio
meanint a matrix of the raw mean log-intensity
gene.anot
badqual integer matrix of number of bad quality observation per gene and replicate. Do not use badqual with different number of replicates in each condition.
qualtol integer. Genes with more than qualtol bad quality observations are removed from the analysis. This argument is ignored is Badqual is NULL
center Logical. If True each array*condition is centered to have a 0 mean log-intensity.
loess.cor Logical. if True then loess transformation of the data is performed. If False no loess transformation is performed
min.rep Minimum number of non-missing value per gene and per condition. Must be at least 2.

Value

A gene expression data object

Author(s)

Paul Delmar


[Package varmixt version 0.2-4 Index]