DaMiR.iTSadjust {DaMiRseq} | R Documentation

## Batch correction of normalized Independent Test Set

### Description

This function aims to perform a batch correction on a normalized independent test set, exploiting the ComBat function of the sva package.

### Usage

    DaMiR.iTSadjust(adj_Learning_set, norm_Ind_Test_set, iTS_batch)

### Arguments

`adj_Learning_set` | A SummarizedExperiment object or a data frame/matrix of adjusted and normalized data, obtained by the DaMiR.SVadjust function.
`norm_Ind_Test_set` | A data frame or a matrix of normalized data. The independent test set is supposed to be already normlaized by the DaMiR.iTSnorm function
`iTS_batch` | (Optional). A factor or a data.frame, containing information regarding experimental batches of the independent test set. Users can ignore this argument, if the independent test set is deemed a single experimental batch.

### Details

The function applied a batch correction procedure to the independent test set, normalized by DaMiR.iTSnorm.

### Value

A matrix containing a normalized and adjusted expression matrix (log2 scale).

### Author(s)

Mattia Chiesa, Luca Piacentini

### References

Jeffrey T. Leek, W. Evan Johnson, Hilary S. Parker, Elana J. Fertig, Andrew E. Jaffe and John D. Storey (2016). sva: Surrogate Variable Analysis. R package version 3.22.0.

### See Also

`ComBat`

### Examples

    # use example data:
    data(SE)

[Package DaMiRseq version 2.2.0 Index]