[BioC] problems with Affy vignette and affybatch objects
Martin Morgan
mtmorgan at fhcrc.org
Tue Oct 31 00:25:38 CET 2006
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
>
> _______________________________________________
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--
Martin T. Morgan
Bioconductor / Computational Biology
http://bioconductor.org
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