tpp2dNormalize {TPP} | R Documentation |
Normalizes fold changes retrieved from 2D-TPP experiment by dividing by the median fold change
tpp2dNormalize(configTable = NULL, data, fcStr = NULL)
configTable |
DEPRECATED |
data |
data frame that contains the data for the 2D-TPP experiment |
fcStr |
DEPRECATED |
A dataframe identical to the input dataframe except that the columns containing the fold change values have been normalized by their median.
# 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"]