vm.analysis.unpaired.step.1 {varmixt} | R Documentation |
First step of analysis in unpaired data case
vm.analysis.unpaired.step.1(geneId, cont, treat, gene.anot = NULL, badqual = NULL, qualtol = NULL, center = TRUE, loess.cor = FALSE, min.rep = 2)
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 |
gene expression data object
Paul Delmar