controlNorm {RNAither} | R Documentation |
Performs a normalization on either positive or negative controls.
controlNorm(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 - 1 or 2, 1 meaning a normalization per experiment, 2 meaning a normalization per plate - 0 or 1, 0 meaning a normalization on the median of negative controls, 1 meaning a normalization on the median of positive controls. Can also be the GeneName of a specific control siRNA
- 1 or 2, 1 meaning the signal values are divided by the median, 2 meaning the median is subtracted from the signal values |
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 <- controlNorm(header, dataset, list(2, 0, "SigIntensity", 1)) newheader <- normres[[1]] newdataset <- normres[[2]]