normalisation {anapuce}

Function to normalize microarray data

Description

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.

Usage

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, ...)

Arguments

fileIN

on optional regular expression contained in names of the files to analyze

Red

name of the column containing the Cy5 values

Green

name of the column containing the Cy3 values

n

number of identificant columns

flag

list of flags values to delete

graph

logical indicating wether to perform graphics

filter.function

function to perform before beginning the normalization

filter.fic

argument passed to filter.funtion - file containing the values of the variable named filter.var to delete

filter.var

argument passed to filter.funtion

sep.write

the field separator string to use in the write.table function

dec.write

the string to use for decimal points in the write.table function

header

a logical value indicating whether the file contains the names of the variables as its first line. Used in the read.table function

sep

the field separator string to use in the read.table function

skip

integer: the number of lines of the data file to skip before beginning to read data.

...

Further arguments to be passed to read.table.

Details

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.

Value

A file resNorm.txt containing the normalized data and if graph=TRUE a file .pdf per array with graphics

Author(s)

J. Aubert

References

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.

See Also

filterByDefault,read.table