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

First step of analysis in unpaired data case

Description

First step of analysis in unpaired data case

Usage

vm.analysis.unpaired.step.1(geneId, cont, treat, 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
cont matrix of gene log-intensity in condition 1. The matrix has one gene per row and one replicate per column
treat matrix of gene log-intensity in condition 1
gene.anot data.frame with further gene anotations
badqual integer matrix of number of bad quality observation per gene and replicate
qualtol integer. Genes with more than qualtol bad quality observations are removed from the analysis. This argument is ignored if Badqual is NULL
center Logical. If True each array is centered to have a 0 mean log-ratio
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

gene expression data object

Author(s)

Paul Delmar


[Package varmixt version 0.2-4 Index]