limmaDS2: Differential expression analysis using limma on the...
In isglobal-brge/dsOmics: DataSHIELD server site Omic functions

limmaDS2

R Documentation

Differential expression analysis using limma on the server-side

Performs differential expression analysis using LIMMA

limmaDS2(Set, res, type, contrasts, coef, annotCols, robust, sort.by)

`Set`	either a `ExpressionSet` or a `RangedSummarizedExperiment`
`type`	...
`contrasts`	...
`coef`	...
`annotCols`	variables from the annotation data used in the output
`robust`	Logical value indicating whether robust method is applied in the eBayes function of limma. Default is FALSE.
`variable_names`	grouping variable used to perform differential expression analysis
`covariable_names`	name of variables used in the adjusted models
`levels`	...
`sva`	should differential expression analysis be adjusted by SVA?
`method`	String indicating the method used in the regression (e.g. lmFit function of limma: "ls" or "robust". (Default: "ls")
`normalization`	String indicating the normalize method used when using voom for RNAseq data (see normalized.method argument in limma::vomm)
`voomQualityWeights`	Logical value indicating whether limma::voomWithQualityWeights should be used instead of limma::voom.
`big`	Logical value indicating whether SmartSVA should be used instead of SVA (TRUE recommended for methylation or when having large number of samples).