[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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