tpp2dNormalize {TPP} | R Documentation

## Median normalization of protein fold changes of 2D-TPP data

### Description

Normalizes fold changes retrieved from 2D-TPP experiment by dividing by the median fold change

### Usage

    tpp2dNormalize(configTable = NULL, data, fcStr = NULL)

### Arguments

`configTable` | DEPRECATED
`data` | data frame that contains the data for the 2D-TPP experiment
`fcStr` | DEPRECATED

### Value

A dataframe identical to the input dataframe except that the columns containing the fold change values have been normalized by their median.

### Examples

    # Preparation:
    data(panobinostat_2DTPP_smallExample)

    # Import data:
    datIn <- tpp2dImport(configTable = panobinostat_2DTPP_config,
                          data = panobinostat_2DTPP_data,
                          idVar = "representative",
                          addCol = "clustername",
                          intensityStr = "sumionarea_protein_",
                          nonZeroCols = "qusm")

    # Compute fold changes:
    datFC <- tpp2dComputeFoldChanges(data = datIn)

    # Perform median normalization:
    datNorm <- tpp2dNormalize(data = datFC)

    # View updated attributes. Now contain field 'fcStrNorm' indicating prefix
    # of the fold change columns after normalization.
    attr(datNorm, "importSettings")["fcStrNorm"]

[Package TPP version 3.20.1 Index]