[BioC] MAPlot

[Mohammad Esad-Djou]

Thanks for your help.  


I have two other questions.  

1.  How can I compare an experiment correctly with a set of experiments in ma.plot?  

is this Ok? (for 7 Expriments)

mat <- exprs( data.exprs )

ma.plot( mat[ , 1] + (mat[ , 2] + mat[ ,3] + mat[ ,4]+ mat[ ,5]+ mat[ ,6]+ mat[ ,7]), mat[ , 1] - (mat[ ,2] - mat[ ,3] - mat[ ,4] - mat[ ,5] - mat[ ,6] - mat[ ,7]) )


2.  How can I save the result of ma.plot directly into a file (e.g. png or JPG...)?  


Thanks,
Mohammad Esad-Djou




ramasamy at cancer.org.uk schrieb am 29.03.05 16:37:38:
> 
> 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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>