tppccrNormalizeToReference {TPP} | R Documentation

## Normalize fold changes of TPP-CCR experiment to a reference column

### Description

Normalize fold changes of TPP-CCR experiment to a reference column (usually that with the lowest concentration) to ensure that the transformation by tppccrTransform yields values between 0 and 1.

### Usage

    tppccrNormalizeToReference(data, refCol = NULL)

### Arguments

`data` | expressionSet object containing the data to be normalized
`refCol` | column number to use as a reference. Will contain only 1s after the normalization.

### Value

List of expressionSet objects storing the normalized fold changes, as well as row and column metadata. In each expressionSet `S`, the fold changes can be accessed by `Biobase::exprs(S)`. Protein expNames can be accessed by `featureNames(S)`. Isobaric labels and the corresponding concentrations are returned by `S$label` and `S$concentration`.

### Examples

    data(hdacCCR_smallExample)
    tppccrData <- tppccrImport(configTable=hdacCCR_config, data = hdacCCR_data)
    tppccrNorm <- tppccrNormalize(data=tppccrData)
    # Normalize to lowest concentration (in the first column):
    tppccrNormToRef <- tppccrNormalizeToReference(data=tppccrNorm, refCol=1)
    # Obtain results per replicate:
    refTransf_replicate1 <- tppccrNormToRef$Panobinostat_1
    head(Biobase::exprs(refTransf_replicate1))
    # Perform transformation:
    tppccrTransformed <- tppccrTransform(data=tppccrNormToRef)
    # Obtain transformed measurements per replicate:
    transf_replicate1 <- tppccrTransformed$Panobinostat_1
    transf_replicate2 <- tppccrTransformed$Panobinostat_2
    # Inspect transformed data in replicate 1:
    effects_replicate1 <- Biobase::featureData(transf_replicate1)$compound_effect
    newData_repl1 <- data.frame(Biobase::exprs(transf_replicate1),
                                  Type=effects_replicate1)[!is.na(effects_replicate1),]

[Package TPP version 3.10.1 Index]