runLimma: runLimma
| runLimma | R Documentation |
runLimma
Description
Run Limma algorithm on the selected conditions. Output is to be used for the interactive display. Adapted from debrowser::runLimma(), a version for non-count RNA data (microarray)
Usage
runLimma(data = NULL, columns = NULL, conds = NULL, params = NULL)
Arguments
data |
A matrix that includes all the expression raw counts, rownames has to be the gene, isoform or region names/IDs. |
columns |
is a vector that includes the columns that are going to be analyzed. These columns has to match with the given data. |
conds |
experimental conditions. The order has to match with the column order |
params |
normfact: Calculate normalization factors to scale the raw library sizes. Values can be "TMM","RLE","upperquartile","none". fitType, fitting method; "ls" for least squares or "robust" for robust regression normBet: Normalizes expression intensities so that the intensities or log-ratios have similar distributions across a set of arrays. datatype: suggest if the data is a count data or not. |
Examples
x <- runLimma()
