tppccrNormalizeToReference: Normalize fold changes of TPP-CCR experiment to a reference...

In DoroChilds/TPP: Analyze thermal proteome profiling (TPP) experiments

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),]
                              

DoroChilds/TPP documentation built on Oct. 31, 2021, 4:38 a.m.