[BioC] MAPlot

[Adaikalavan Ramasamy]

See comments below.

On Tue, 2005-03-29 at 16:13 +0100, Mohammad Esad-Djou wrote: 
> Hello, 
> 
> I wrote a small program for MAS5.0:
> 
> 
> library(affy)
> library(affydata)
> 
> data.raw <- ReadAffy(filenames="./R/ME_cel/Expt1_R1.CEL",
> 			     "./R/ME_cel/Expt2_R1.CEL")


This is produce a syntax error. Try this

ReadAffy( filenames=c("Expt1_R1.CEL", "Expt2_R1.CEL"), 
          celfile.path="./R/ME_cel/")



> data.exprs <- mas5(data.raw, sc=150)
> rm(data.raw)
> data.out <- cbind(483, "ME-mas5", "ME_Affy MAS5 Transformation (R)", data.exprs at exprs, 0)
> write.table(data.out, file="./R/ME_data/aggregation_1.dat", sep="\t", col.names=NA, quote=FALSE)
> rm(data.exprs, data.out)

I find it easier to with the exprSet which can retrieved as

 mat <- exprs( data.exprs )

help.search("MA plot") suggests ma.plot in the affy package. You will
have to decide what "M" and "A" means with affymetrix data. M could be
difference in the two arrays and A could be the average

 ma.plot( mat[ , 1] + mat[ ,2], mat[ , 1] - mat[ ,2] )


> The result is written in aggregation_1.dat.  Now, I would like to visualize result file with MAPlot, but I don't know, which intermediate steps are necessary.  What can I do?
> 
> Thanks,
> Mohammad Esad-Djou
> 
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