[BioC] From eSet to AffyBatch Object

[Jenny Drnevich]

Hi Boris,

For the hist, try plotHist() in the affycoretools package to 
automagically get a legend and colors, or you can do it the way 
Martin suggested which lets you have more control over what is 
plotted. I'm not sure why you would want to use the image on an 
ExpressionSet object, but the affyPLM package has a good way to plot 
the residuals left after fitting a pre-processing algorithm so you 
can more easily see spatial effects on your arrays; see the QC 
assessment vignette of affyPLM (athough it's missing in my current R 
installation - I'll post a separate thread about it). Finally, for 
the boxplot you can do:

 > boxplot(data.frame(exprs(e))

Cheers,
Jenny

At 11:48 PM 3/2/2009, Martin Morgan wrote:
>Hi Boris --
>
>Boris Umylny <umylny at apbri.org> writes:
>
> > Hi,
> >
> > I am working with affy library from Bioconductor 2.3.
> >
> > The library contains functions (hist, image and boxplot) that 
> work directly on
> > AffyBatch object, but apparently not on ExpressionSet/eSet 
> object.  After I
> > use rma, expresso or mas5 to do background correction and 
> normalization I get
> > an eSet object, which appears to be incompatible with these 
> functions.  If I
> > call hist(exprs(e)), where e is an ExpressionSet object, I get a 
> plot of the
> > first array only.
> >
> > Is there a Bioconductor library (other than geneplotter which 
> apparently does
> > not) that provides these functions on eSet/ExpressionSet object?
>
>Others will probably point to specific packages implementing plotting
>methods for expression data, but I find myself doing things more
>directly, typically using the lattice package
>
>   library(lattice)
>   library(Biobase)
>   data(sample.ExpressionSet)
>   eset <- sample.ExpressionSet   # easier to type!
>   df <- data.frame(Expression=as.vector(exprs(eset)),
>                    Sample=sampleNames(eset)[col(eset)])
>   densityplot(~log2(Expression)|Sample, df, plot.points=FALSE)
>
>or
>
>   densityplot(~log2(Expression), group=Sample, df, plot.points=FALSE)
>
> > Is there a way to get an AffyBatch object from eSet object to make use of
> > these functions?
>
>An AffyBatch and an ExpressionSet are conceptually different ('raw'
>vs. preprocessed data) so trying to convert back and forth at will
>doesn't really make sense.
>
>Martin
>
> > Thank you in advance for your help.
> >
> >
> > Sincerely,
> >
> >
> > Boris Umylny
> >
> > _______________________________________________
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>
>--
>Martin Morgan
>Computational Biology / Fred Hutchinson Cancer Research Center
>1100 Fairview Ave. N.
>PO Box 19024 Seattle, WA 98109
>
>Location: Arnold Building M2 B169
>Phone: (206) 667-2793
>
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
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e-mail: drnevich at illinois.edu