lowessNorm {RNAither} | R Documentation |
Performs a plate-wise lowess normalization of the data.
lowessNorm(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 used as channel 1 (colname4ch1) - a character string specifying the column used as channel 2 (colname4ch2) - optionally: the smoother span (smSpan) of the lowess function. This gives the proportion of points which influence the smooth at each value. Larger values give more smoothness. Defaults to 2/3. |
Corrects intensity values in case the values of ch2 decrease with the increase of ch1 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 <- lowessNorm(header, dataset, list("NbCells","SigIntensity")) newheader <- normres[[1]] newdataset <- normres[[2]]