[BioC] From eSet to AffyBatch Object

[Boris Umylny]

Thank you very much for your help!

I wound up using Martin's suggestion for density and boxplots.  As Jenny 
pointed out it does not make much sense to run image on an ExpressionSet.  
However, that does require users to utilize AffyRead even if they are 
processing their data with just.rma.  However, thats not a major obtacle.

I did find a strange error with just.rma when reading gzipped CEL files from 
GSE10641 (samples GSM268225, GSM268224, GSM268223, GSM268222, GSM268221, 
GSM268214, GSM268213, GSM268212, GSM268211, GSM268210, GSM268209, GSM268226, 
GSM268233, GSM268234, GSM268235, GSM268236, GSM268237, GSM268238) with 
normalize=FALSE:

Error in dimnames(x) <- dn : 'dimnames' applied to non-array

and ExpressionSet was not created.

When I used AffyRead and rma (with normalize=FALSE), it worked fine.

I am using R 2.8.1, Bioconductor 2.3 and including: 

library(affy)
library(geneplotter)
library(lattice)
library(Biobase)


Thank you again for your help!


Sincerely,


Boris Umylny



On Tuesday 03 March 2009 02:48:13 pm 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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