[BioC] From Limma to SAM

Gordon Smyth smyth at wehi.edu.au
Sat Dec 6 00:15:05 MET 2003

 > Gordon wrote:
 >>This isn't an error in limma of course, rather you have tried to use a
 >>function (write.table) on an inappropriate object. Do you want to
 >> output
 >>the normalized log-ratios? If so, you might try
 >>write.table(MA$M, file="your_file.txt",sep="\t")
 > I've tried write.table(MA$M, file="your_file.txt",sep="\t") and it's OK,
 > but i'd like to output my normalized-between-array (unlogged or Log2)
 > data to SAM. Is it possible?

On reading your question again, I'm guessing that you're wanting the 
normalized single-channel red and green intensities. Is this right? If so, 
you can get them from


(see the last section of the Limma User's Guide) where MA is the normalized 
MAList object, then write RG$R and RG$G to file. Or possibly form 
cbind(RG$G,RG$R) and write that to one file.

I do not know what the SAM software wants as input. Checking that is of 
course your responsibility.


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