quantileNormalization {RNAither} | R Documentation |
Quantile normalization (see References)
quantileNormalization(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 |
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" |
B.M. Bolstad, R.A. Irizarry, M. Astrand, and T.P. Speed. A Comparison of Normalization Methods for High Density Oligonucleotide Array Data Based on Variance and Bias. Bioinformatics, 19(2): 185-193, 2003
data(exampleHeader, package="RNAither") data(exampleDataset, package="RNAither") normres <- quantileNormalization(header, dataset, list(2, "SigIntensity")) newheader <- normres[[1]] newdataset <- normres[[2]]