vm.analysis.paired.step.1 {varmixt} | R Documentation |
Function to do the first step of analysis in paired data case
vm.analysis.paired.step.1(geneId, ratio, meanint = NULL, gene.anot = NULL, badqual = NULL, qualtol = NULL, center = TRUE, loess.cor = FALSE, min.rep = 2)
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. |
A gene expression data object
Paul Delmar