[BioC] M vs A plots of affymetrix data

[Ben Bolstad]

as I said. You need affyPLM loaded, not just affy.


On Thu, 2006-03-09 at 15:33 +0000, michael watson (IAH-C) wrote:
> Hi Ben
>  
> Thanks for the help :)
>  
> When I tried following your example on the affybatch.example data set:
>  
> eset.rma <- rma(affybatch.example)
> MAplot(eset.rma)
>  
> I get an error about there being no direct or inherited method.
>  
> Mick
> 
> ________________________________
> 
> From: Ben Bolstad [mailto:bmb at bmbolstad.com]
> Sent: Thu 09/03/2006 3:15 PM
> To: michael watson (IAH-C)
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] M vs A plots of affymetrix data
> 
> 
> 
> 
> > I realise that I have to take two arrays pairwise to get my ratio(M)
> > and average(A), but does anyone know if these plots are generally at
> > the probe level or at the gene level?
> 
> You can do them at the probe or probeset level. In the document you
> referenced some were done at the probe level and some were done at the
> probeset level.
> 
> 
> > If at the probe level, are they the ratio and average of just the PM
> > intensities?
> 
> Typically just PM intensities.
> 
> 
> > Also, when I read data in using ReadAffy(), are the PM and MM
> > intensities raw or on a logged scale?  If I then perform rma() or
> > mas5(), are the gene level intensities on a log scale?  This is
> > important, as I need to figure out how to calculate the ratio and
> > average
> 
> ReadAffy() returns intensities on the natural scale. rma() expression
> values are on the log2 scale. mas5() values are natural scale.
> 
> You of course are free to construct these yourself, but there are some
> buit-in functions for doint this also. If you have affyPLM loaded you
> should be able to use the MAplot() function applied to either
> AffyBatches or exprSets.  eg
> 
> 
> library(affyPLM)
> data(Dilution) # Dilution is an AffyBatch.
> 
> # each array against a median-wise synthetic reference array
> MAplot(Dilution,ylim=c(-2,2))
> 
> # comparing arrays 2:4 with array 1
> MAplot(Dilution,ylim=c(-2,2),ref=1,which=2:4)
> 
> 
> # MA plot comparing 1 to 4
> MAplot(Dilution,ylim=c(-2,2),ref=1,which=4)
> 
> 
> #the infamous pairwise plot
> MAplot(Dilution,pairs=TRUE)
> 
> 
> eset.rma <- rma(Dilution)
> 
> #examine to see that they are on log2 scale
> exprs(eset.rma)[1:5,] 
> 
> # each array against a median-wise synthetic reference array
> MAplot(eset.rma)
> 
> 
> eset.mas5 <- mas5(Dilution)
> 
> #examine to see on natural scale
> exprs(eset.mas5)[1:5,]
> 
> 
> #need to tell it to take the log if supplying natural scale
> #expression values.
> MAplot(eset.mas5,log=TRUE)
> 
> 
> 
> 
> --
> Ben Bolstad <bmb at bmbolstad.com>
> http://bmbolstad.com
> 
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