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),]