| tppccrNormalizeToReference {TPP} | R Documentation |
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.
tppccrNormalizeToReference(data, refCol = NULL)
data |
expressionSet object containing the data to be normalized |
refCol |
column number to use as a reference. Will contain only 1s after the normalization. |
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.
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),]