Execute edgeR expression Analisys

Execute edgeR expression Analisys

Usage

runLimma(
  countMatrix,
  numberReplics,
  designExperiment,
  methodNorm = "TMM",
  methodAdjPvalue = "BH",
  numberTopTable = 1e+06
)

Arguments

countMatrix

either a matrix of raw (read) counts.

numberReplics

number of replicate (technical or biologcal) integer

designExperiment

replicate and treatment by samples

methodNorm

normalization method to be used

methodAdjPvalue

correction method, a character string. Can be abbreviated.

numberTopTable

maximum number of genes to list

Value

limma report in data Frame fromat

Examples

data(gse95077)
treats = c("BM", "JJ")
toolResult <- NULL
toolResult$limma <- runLimma(countMatrix = gse95077,
                             numberReplics = 3,
                             designExperiment = rep(treats, each = 3))
#> Removing intercept from test coefficients