| centralize {StabPerf} | R Documentation |
Calls the external Java application in Centralizer.jar to normalize the given data.
centralize(data, q=.98, MinInt=NA, MaxInt=NA)
data |
matrix or data.frame to be normalized. Samples in columns, variables in rows. |
q |
numeric. Which middle quantiles of the data to consider. E.g. q=.50 will set MinInt to the 25th quantile of data' and MaxInt to the 75th quantile of data |
MinInt |
numeric. Minimum value to be considered in centralization. |
MaxInt |
numeric. Maximum value to be considered in centralization. |
The data are written to a temporary text file before being read in by the external application. The java virtual machine is started and stopped by each call to this function. I.e. it is very inefficient and should not be used in tight loops.
Using this function requires installing the Centralizer.jar application in the lib subdirectory of the root directory of this package.
data |
data.frame. Normalized data. |
Zien, A., Aigner, T., Zimmer, R., and Lengauer, T. (2001). Centralization: a new method for the normalization of gene expression data. Bioinformatics, 17 Suppl 1:S323 31.
normed <- centralize(data, MinInt=0.01, MaxInt=3.0)