[BioC] From Limma to SAM

[Gordon Smyth]

 > 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

RG <- RG.MA(MA)

(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.

Gordon