for normalization of microarray data

I want to normalize data using RMA 开发者_开发技巧in R package. but there has problem it does not read .txt file. Please tell me, "what I do for normalizing data from .txt file?" reply please

Basically all normalization methods in Bioconductor are based on the AffyBatch class. Therefore, you have to read your textfile (probably a matrix) and create an AffyBatch manually:

AB <- new("AffyBatch", exprs = exprs, cdfName = cdfname, phenoData = phenoData,...)

RMA needs ExpressionSet structure. After reading the file (read.table()) and cleaning colnames and row.names convert the file to matrix and use:

a<-ExpressionSet(assayData=matrix)

If didnt work, import your *.txt data to flexarray software which can read it and do rma.

This may work.

I use normalizeQuantiles() function from Limma R package:

library(limma)


mydata <- read.table("RDotPsoriasisLogNatTranformedmanuallyTABExport.tab", sep = "\t", header = TRUE) # read from file


b = as.matrix(cbind(mydata[, 2:5], mydata[, 6:11])) # set the numeric data set

m = normalizeQuantiles(b, ties=TRUE) # normilize

mydata_t <- t(as.matrix(m)) # transpose if you need