varAdjust {RNAither} | R Documentation |
Divides the intensity values by their median absolute deviation (of the experiment or of the plate)
varAdjust(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 screen, 2 a normalization per plate - a flag specifying whether controls should be excluded for the computation of the median absolute deviation (1) or not (0). |
Divides the intensity values by their median absolute deviation (of the experiment or of the plate).
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 of the dataset with the suffix ".old" |
data(exampleHeader, package="RNAither") data(exampleDataset, package="RNAither") normres <- varAdjust(header, dataset, list(1, "SigIntensity", 1)) newheader <- normres[[1]] newdataset <- normres[[2]]