divNorm {RNAither} | R Documentation |
Normalization with the mean, median, or any other function.
divNorm(header, dataset, listOfArgs)
header |
the header of a dataset file generated with generateDatasetFile |
dataset |
an R data frame generated with generateDatasetFile |
listOfArgs |
a list containing:
- a character string specifying the column whose values will be used for normalization - a function to be used for the normalization, e.g. mean , median , ...
- 1 or 2, 1 meaning a normalization per experiment, 2 meaning a normalization per plate - 1 or 2, 1 meaning the normalization is achieved by a division of the intensity values by the outcome of funname , 2, meaning by a substraction
- a flag specifying whether controls should be excluded for the computation of the result of the function specified in the first element (1) or not (0). |
Returns a list containing:
header |
the new header (with an added entry about the normalization procedure in the comments) |
dataset |
the new dataset with normalized values. The old values are saved in an extra column with the suffix ".old" |
data(exampleHeader, package="RNAither") data(exampleDataset, package="RNAither") normres <- divNorm(header, dataset, list(median, 2, 1, "SigIntensity", 1)) newheader <- normres[[1]] newdataset <- normres[[2]]