Execute NOISeq gene Expression analysis

Usage

runNoiSeq(
  countMatrix,
  designExperiment,
  groups = c(""),
  normParm = "rpkm",
  kParam = 0.5,
  factorParam = c("Tissue"),
  lcParam = 0,
  replicatesParam = "technical",
  condExp = c("")
)

Arguments

countMatrix: either a matrix of raw (read) counts.
designExperiment: replicate and treatment by samples.
groups: text list separated by comma, name of samples or treatment.
normParm: Normalization method t can be one of "rpkm" (default), "uqua" (upper quartile), "tmm" (trimmed mean of M) or "n" (no normalization).
kParam: Counts equal to 0 are replaced by k. By default, k = 0.5
factorParam: A string indicating the name of factor whose levels are the conditions to be compared.
lcParam: Length correction is done by dividing expression by length^lc. By default, lc = 0
replicatesParam: In this argument, the type of replicates to be used is defined: "technical", "biological" or "no" replicates. By default, "technical" replicates option is chosen.
condExp: A vector containing the two conditions to be compared by the differential expression algorithm (needed when the factor contains more than 2 different conditions).

Value

A data.frame with output of noiseqOut@results

Examples

data(gse95077)
treats = c("BM", "JJ")
toolResult <- NULL
toolResult$noiseq <- runNoiSeq(countMatrix = gse95077,
                               designExperiment = rep(treats, each = 3))
#> [1] "Computing (M,D) values..."
#> [1] "Computing probability of differential expression..."