Hi Boris --
Boris Umylny <umylny at="" apbri.org=""> writes:
> Thank you very much for your help!
> I wound up using Martin's suggestion for density and boxplots. As
> pointed out it does not make much sense to run image on an
> However, that does require users to utilize AffyRead even if they
> processing their data with just.rma. However, thats not a major
> I did find a strange error with just.rma when reading gzipped CEL
> GSE10641 (samples GSM268225, GSM268224, GSM268223, GSM268222,
> GSM268214, GSM268213, GSM268212, GSM268211, GSM268210, GSM268209,
> GSM268233, GSM268234, GSM268235, GSM268236, GSM268237, GSM268238)
> 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.
Unfortunately, I don't see this problem when I try with R 2.8.0 or
R-devel. To track it down further it would really help to see the
output of sessionInfo() (after following the instructions to update
packages at http://bioconductor.org/docs/install/
and confirming that
the error still occurs) and the precise command that you used. Here's
> f <- c("GSM268225", "GSM268224", "GSM268223", "GSM268222",
"GSM268221", "GSM268214", "GSM268213", "GSM268212", "GSM268211",
"GSM268210", "GSM268209", "GSM268226", "GSM268233", "GSM268234",
"GSM268235", "GSM268236", "GSM268237", "GSM268238")
> f <- paste(f, ".CEL.gz", sep="")
> all(f %in% list.files())
> res <- justRMA(filenames=f, normalize=FALSE)
R version 2.8.0 Patched (2008-11-10 r46882)
attached base packages:
 tools stats graphics utils datasets
other attached packages:
 rat2302cdf_2.3.0 affy_1.20.2 Biobase_2.2.2
loaded via a namespace (and not attached):
 affyio_1.10.1 preprocessCore_1.4.0
> I am using R 2.8.1, Bioconductor 2.3 and including:
> Thank you again for your help!
> 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
>> > directly on AffyBatch object, but apparently not on
>> > object. After I use rma, expresso or mas5 to do background
>> > and normalization I get an eSet object, which appears to be
>> > 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
>> > does not) that provides these functions on eSet/ExpressionSet
>> Others will probably point to specific packages implementing
>> methods for expression data, but I find myself doing things more
>> directly, typically using the lattice package
>> eset <- sample.ExpressionSet # easier to type!
>> df <- data.frame(Expression=as.vector(exprs(eset)),
>> densityplot(~log2(Expression)|Sample, df, plot.points=FALSE)
>> densityplot(~log2(Expression), group=Sample, df,
>> > 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.
>> > Thank you in advance for your help.
>> > Sincerely,
>> > Boris Umylny
>> > _______________________________________________
>> > Bioconductor mailing list
>> > Bioconductor at stat.math.ethz.ch
>> > https://stat.ethz.ch/mailman/listinfo/bioconductor
>> > Search the archives:
>> > http://news.gmane.org/gmane.science.biology.informatics.conductor
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