[BioC] problems with Affy vignette and affybatch objects
Jenny Drnevich
drnevich at uiuc.edu
Tue Oct 31 17:58:54 CET 2006
Hi all,
Thanks to Martin, Seth, and Jim for pointing out that my trouble was
because I was using objects that had been created with a previous version
of R and Bioconductor. I have seen this issue mentioned before on the
mailing list, but I didn't think about it being the cause of my problems
because 1) I mistakenly thought I was working with new data, instead of
realizing I was checking on something in a previous analysis, and 2) in my
mind the postings before had to do with people using the development
versions of R and Bioconductor (I remembered that 'updatePackages' at that
time was in the development version of Biobase). Now, I know my memory is
faulty, so I went back and looked at the release news items for R and
Bioconductor. There was nothing in the Bioconductor 1.9 news release to
indicate that previous data objects should be re-made or updated with
'updateObjects'. I did find something in the R news (which I usually don't
read - I know, shame on me) in the CHANGES TO S4 METHODS section, but it
would not be apparent to the _typical_ PC Bioconductor user, if I may so
stereotype myself and others this way, that this applies to AffyBatch,
eSet, etc. objects. Was there an announcement from Bioconductor in an
obvious place along the lines that due to changes in R for S4 classes, data
objects made with previous versions should be re-created or updated using
'updateObjects'? Perhaps there should have been, but if there was one and I
just missed it, I apologize.
'updateObjects' appeared to work fine on my AffyBatch object, but when I
used it on an exprSet object created by 'gcrma', the updated object was
still an exprSet object. I thought stuff was going to switch to
expressionSet objects - what's the difference between an exprSet and an
expressionSet? Or is this something the casual user doesn't need to know
about for now?
Thanks,
Jenny
P.S. I did finally get my own postings to the list, after about 5-8 hour
delay... we'll see how long it take me to get this one!
At 05:25 PM 10/30/2006, Martin Morgan wrote:
>Hi Jenny --
>
>I think the problem is that your data 'raw' was created with R 2.3.1
>or earlier. R 2.4.0 introduced a change to the way these data
>structures are represented, and unfortunately did so in a way that
>messes up the 'show' methods. Make a backup of your data, then try
>this:
>
>library(affy)
>load("raw.rda") # load your data
>rawUpdt <- updateObject(rawUpdt)
>
>rawUpdt should now behave better. Check it carefully (you might try
>str(rawUpdt) to get an overview of the contents) to see that
>updateObject has not done anything bad -- it's a general purpose
>function from Biobase, rather than a function written to handle
>AffyBatch objects in particular.
>
>The problem with the vignette is that the affybatch.example data is
>also in the old format; we'll try to fix that from this end.
>
>There were some changes to affy in the last release cycle -- these
>were generally documentation changes or bug fixes that appear to be
>minor. More detail can be found in the links from the page at
>
>http://bioconductor.org/news
>
>Thanks for the report; please let me know if you encounter problems
>updating your data.
>
>Martin
>
>Jenny Drnevich <drnevich at uiuc.edu> writes:
>
> > Hi,
> >
> > There's some problem with the default value for affybatch objects (if this
> > is the correct description) that's appeared in affy 1.12.0, which also can
> > be seen in the affy vignette. Previously, when I typed in the name of an
> > affybatch object at the command line, I'd get the same output as if I had
> > put 'show(abatch)':
> >
> > > raw
> > AffyBatch object
> > size of arrays=602x602 features (53806 kb)
> > cdf=RAE230A (15923 affyids)
> > number of samples=19
> > number of genes=15923
> > annotation=rae230a
> >
> > > show(raw)
> > AffyBatch object
> > size of arrays=602x602 features (53806 kb)
> > cdf=RAE230A (15923 affyids)
> > number of samples=19
> > number of genes=15923
> > annotation=rae230a
> >
> > > sessionInfo()
> > Version 2.3.1 Patched (2006-08-06 r38829)
> > i386-pc-mingw32
> >
> > attached base packages:
> > [1] "splines" "tools" "methods" "stats" "graphics" "grDevices"
> > [7] "utils" "datasets" "base"
> >
> > other attached packages:
> > rae230acdf affyQCReport simpleaffy reposTools made4
> > "1.12.0" "1.10.0" "2.6.0" "1.10.0" "1.6.0"
> > scatterplot3d ade4 affyPLM gcrma matchprobes
> > "0.3-24" "1.4-1" "1.8.0" "2.4.1" "1.4.0"
> > affydata affycoretools GOstats Category hgu95av2
> > "1.8.0" "1.4.0" "1.6.0" "1.4.1" "1.12.0"
> > KEGG multtest genefilter survival xtable
> > "1.12.0" "1.10.2" "1.10.1" "2.26" "1.3-2"
> > RBGL annotate GO graph Ruuid
> > "1.8.1" "1.10.0" "1.12.0" "1.10.6" "1.10.0"
> > limma affy affyio Biobase RWinEdt
> > "2.7.9" "1.10.0" "1.0.0" "1.10.1" "1.7-4"
> >
> > However, now when I just type in the name of the affybatch object, the
> > entire contents of the affybatch object is output! (current sessionInfo
> > below). This is also in the vignette (October 3, 2006), on page 11-251
> (did
> > no one notice the vignette was 271 pages long?!?). I had noticed that the
> > previous vignette from affy 1.10.0 (April 25, 2006) was also 271 pages
> long
> > when called from my installation, but at the time when I went back and
> > checked on the Bioconductor website, the vignette listed there was the
> > right length. I thought the problem had been corrected, and since I wasn't
> > having any trouble typing in the name of the affybatch object to get the
> > summary, I didn't report it.
> >
> > One last thing - were there no changes to affy for the Bioconductor 1.9
> > release? The beginning of the vignette (Oct 3, 2006) still has listed
> > 'Changes for affy in BioC 1.8 release' in section 2, along with all the
> > same information as in the previous vignette.
> >
> > Thanks,
> > Jenny
> >
> > >raw
> > #many, many, many lines deleted...
> > a18 15 4 1
> > a19 15 4 2
> > a20 15 5 1
> > a21 15 5 2
> > Slot "varLabels":
> > Slot "varLabels":$Week
> > [1] "Week"
> >
> > Slot "varLabels":$Group
> > [1] "Group"
> >
> > Slot "varLabels":$Rep
> > [1] "Replicate"
> >
> > Slot "varMetadata":
> > NULL data frame with 0 rows
> >
> > > show(raw)
> > AffyBatch object
> > size of arrays=602x602 features (53806 kb)
> > cdf=RAE230A (15923 affyids)
> > number of samples=19
> > number of genes=15923
> > annotation=rae230a
> >
> > > sessionInfo()
> > R version 2.4.0 (2006-10-03)
> > i386-pc-mingw32
> >
> > locale:
> > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> > States.1252;LC_MONETARY=English_United
> > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> >
> > attached base packages:
> > [1] "splines" "tools" "methods" "stats" "graphics" "grDevices"
> > [7] "utils" "datasets" "base"
> >
> > other attached packages:
> > rae230acdf affyQCReport simpleaffy made4 scatterplot3d
> > "1.14.0" "1.12.0" "2.8.0" "1.8.0" "0.3-24"
> > ade4 affyPLM gcrma matchprobes affydata
> > "1.4-2" "1.10.0" "2.6.0" "1.6.0" "1.10.0"
> > affycoretools biomaRt RCurl XML GOstats
> > "1.6.0" "1.8.0" "0.7-0" "0.99-93" "2.0.0"
> > Category genefilter survival KEGG RBGL
> > "2.0.0" "1.12.0" "2.29" "1.14.0" "1.10.0"
> > annotate GO graph limma affy
> > "1.12.0" "1.14.0" "1.12.0" "2.9.1" "1.12.0"
> > affyio Biobase RWinEdt
> > "1.2.0" "1.12.0" "1.7-5"
> > >
> >
> >
> >
> > 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
> > 1201 W. Gregory Dr.
> > Urbana, IL 61801
> > USA
> >
> > ph: 217-244-7355
> > fax: 217-265-5066
> > e-mail: drnevich at uiuc.edu
> >
> > _______________________________________________
> > 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
>
>--
>Martin T. Morgan
>Bioconductor / Computational Biology
>http://bioconductor.org
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