Hi guys,

Could you suggest me a way to normalize Illumina expression beadchip data?

For example, starting from the GSE32025_non-normalized.txt.gz file, could you suggest me some few steps (preferentially in R) to finally obtain a normalized data matrix as for Affymetrix RMA normalisation? I suppose this is an intensity "count" matrix. When I started reading it using limma and the following instruction: idata <- read.ilmn("GSE32025_non-normalized.txt",probeid = "ID_REF",expr="SKBR"), the following error appeared:

Error in readGenericHeader(fname, columns = expr, sep = sep) : 
  Specified column headings not found in file
In addition: Warning message:
In grep(a, txt) : input string 1 is invalid in this locale

I don't know how to deal with this error since this is the first time for me that I analyse this kind of data.

Can anyone help me please?

Thank you in advance

e.