Performs the data normalization using a general loess and a block effect correction via the subtraction of the median by block if there is a Block column.
normalisation(fileIN = NULL, Red = "F635.Median", Green = "F532.Median",
n = 3, flag = -100, graph = TRUE, filter.function = filterByDefault,
filter.fic = NULL, filter.var = NULL, sep.write = "\t", dec.write = ".",
header = TRUE, sep = "\t", skip = 0, ...)on optional regular expression contained in names of the files to analyze
name of the column containing the Cy5 values
name of the column containing the Cy3 values
number of identificant columns
list of flags values to delete
logical indicating wether to perform graphics
function to perform before beginning the normalization
argument passed to filter.funtion - file containing the values of the variable named filter.var to delete
argument passed to filter.funtion
the field separator string to use in the write.table function
the string to use for decimal points in the write.table function
a logical value indicating whether the file contains the names of the variables as its first line. Used in the read.table function
the field separator string to use in the read.table function
integer: the number of lines of the data file to skip before beginning to read data.
Further arguments to be passed to read.table.
A file resNorm.txt containing the normalized data and if graph=TRUE a file .pdf per array with graphics
By default fileIN=NULL and the files to analyze have to be choosen among all the files in the working directory. If fileIN is not NULL, only file names which match the regular expression fileIN will be proposed to the normalization step.
Yang, Y., Dudoit, S., Luu, P., Lin, D., Peng, V., Ngai, J. and Speed, T., (2002), Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation, Nucleic Acids Research 30.