[BioC] MAPlot

[Adaikalavan Ramasamy]

See below.

On Tue, 2005-03-29 at 19:33 +0100, Mohammad Esad-Djou wrote:
> 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]) )
> 

Yikes ! What are you trying to do here ? Do you know about rowSums() and
rowMeans(). The following is not what you have written above but what I
think you want.

rm27 <- rowMeans( mat[ , 2:7] )
ma.plot( mat[ ,1] - rm27, mat[ ,1] + rm27 )

I cannot comment on whether this is sensible because I never used
ma.plot() on Affymetrix data. Perhaps other members of the mailing list
might wish to comment on this.


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

Two ways.

a) With some forsight

 jpeg(file="lala.jpg")
 plot( 1:10 )
 dev.off()

b) or with hindsight

 plot(1:10)
 dev.copy2eps( file="lala.eps" )


> 
> 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
> > > 
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor at stat.math.ethz.ch
> > > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > > 
> > 
> 
> 
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