[BioC] From eSet to AffyBatch Object

Tue Mar 10 04:30:20 CET 2009

Martin,

Let me apologize in advance if I made a silly mistake - my programming skills 
are fairly limited.

I've attached two files to this e-mail.  R.in contains the R script and R.out 
is the screen capture of the output produced by the script.  R command was 
invoked with "--vanilla".

Both files are in Linux text forma.  I am using SUSE Linix 10.3.

Sincerely,

Boris Umylny

On Friday 06 March 2009 11:47:34 pm Martin Morgan wrote:
> 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 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.
>
> 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
> mine...
>
> > setwd("~/tmp/GEO")
> > 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())
>
> [1] TRUE
>
> > res <- justRMA(filenames=f, normalize=FALSE)
> > sessionInfo()
>
> R version 2.8.0 Patched (2008-11-10 r46882)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-
>8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_AD
>DRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] tools     stats     graphics  utils     datasets
> grDevices methods
> [8] base
>
> other attached packages:
> [1] rat2302cdf_2.3.0 affy_1.20.2      Biobase_2.2.2
>
> loaded via a namespace (and not attached):
> [1] affyio_1.10.1        preprocessCore_1.4.0
>
> Martin
>
> > 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
> >> >
> >> > _______________________________________________
> >> > 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

-------------- next part --------------
library(affy)
library(geneplotter)
library(lattice)
library(Biobase)
e <- just.rma("/home/umylny/tmp/rat_cel/GSM268209.CEL.gz","/home/umylny/tmp/rat_cel/GSM268210.CEL.gz","/home/umylny/tmp/rat_cel/GSM268211.CEL.gz","/home/umylny/tmp/rat_cel/GSM268212.CEL.gz","/home/umylny/tmp/rat_cel/GSM268213.CEL.gz","/home/umylny/tmp/rat_cel/GSM268214.CEL.gz","/home/umylny/tmp/rat_cel/GSM268221.CEL.gz","/home/umylny/tmp/rat_cel/GSM268222.CEL.gz","/home/umylny/tmp/rat_cel/GSM268223.CEL.gz","/home/umylny/tmp/rat_cel/GSM268224.CEL.gz","/home/umylny/tmp/rat_cel/GSM268225.CEL.gz","/home/umylny/tmp/rat_cel/GSM268226.CEL.gz","/home/umylny/tmp/rat_cel/GSM268233.CEL.gz","/home/umylny/tmp/rat_cel/GSM268234.CEL.gz","/home/umylny/tmp/rat_cel/GSM268235.CEL.gz","/home/umylny/tmp/rat_cel/GSM268236.CEL.gz","/home/umylny/tmp/rat_cel/GSM268237.CEL.gz","/home/umylny/tmp/rat_cel/GSM268238.CEL.gz", normalize=FALSE)
sessionInfo()

-------------- next part --------------
WARNING: ignoring environment value of R_HOME

R version 2.8.1 (2008-12-22)
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ISBN 3-900051-07-0

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> library(affy)
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

> library(geneplotter)
Loading required package: lattice
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: xtable
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
> library(lattice)
> library(Biobase)
> e <- just.rma("/home/umylny/tmp/rat_cel/GSM268209.CEL.gz","/home/umylny/tmp/rat_cel/GSM268210.CEL.gz","/home/umylny/tmp/rat_cel/GSM268211.CEL.gz","/home/umylny/tmp/rat_cel/GSM268212.CEL.gz","/home/umylny/tmp/rat_cel/GSM268213.CEL.gz","/home/umylny/tmp/rat_cel/GSM268214.CEL.gz","/home/umylny/tmp/rat_cel/GSM268221.CEL.gz","/home/umylny/tmp/rat_cel/GSM268222.CEL.gz","/home/umylny/tmp/rat_cel/GSM268223.CEL.gz","/home/umylny/tmp/rat_cel/GSM268224.CEL.gz","/home/umylny/tmp/rat_cel/GSM268225.CEL.gz","/home/umylny/tmp/rat_cel/GSM268226.CEL.gz","/home/umylny/tmp/rat_cel/GSM268233.CEL.gz","/home/umylny/tmp/rat_cel/GSM268234.CEL.gz","/home/umylny/tmp/rat_cel/GSM268235.CEL.gz","/home/umylny/tmp/rat_cel/GSM268236.CEL.gz","/home/umylny/tmp/rat_cel/GSM268237.CEL.gz","/home/umylny/tmp/rat_cel/GSM268238.CEL.gz", normalize=FALSE)
Error in dimnames(x) <- dn : 'dimnames' applied to non-array
In addition: Warning message:
In just.rma("/home/umylny/tmp/rat_cel/GSM268209.CEL.gz", "/home/umylny/tmp/rat_cel/GSM268210.CEL.gz",  :
  Incompatible phenoData object. Created a new one.

> sessionInfo()
R version 2.8.1 (2008-12-22)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] rat2302cdf_2.3.0    geneplotter_1.20.0  annotate_1.20.1
[4] xtable_1.5-4        AnnotationDbi_1.4.3 lattice_0.17-17
[7] affy_1.20.2         Biobase_2.2.2

loaded via a namespace (and not attached):
[1] affyio_1.10.1        DBI_0.2-4            grid_2.8.1
[4] KernSmooth_2.22-22   preprocessCore_1.4.0 RColorBrewer_1.0-2
[7] RSQLite_0.7-1
>                                                     