[BioC] problems with affy function indexProbes on Mac

[James W. MacDonald]

Hi Jenny,

drnevich at uiuc.edu wrote:
> Hi all,
> 
> I'm working with a friend who just installed R and Bioconductor
> yesterday using the precompiled Max OSX binaries and biocLite. We're
> having some problems with indexProbes, and I can't see an obvious
> reason why. Archives weren't helpful.
> 
> 
> 
>> library(affy)
> 
> Loading required package: Biobase Loading required package: tools
> 
> Welcome to Bioconductor
> 
> Vignettes contain introductory material. To view, type 
> 'openVignette()' or start with 'help(Biobase)'. For details on
> reading vignettes, see the openVignette help page.
> 
> Loading required package: affyio
> 
>> rawdata <- ReadAffy()
> 
> 
>> library(made4)
> 
> Loading required package: ade4 Loading required package:
> scatterplot3d
> 
>> overview(rawdata)
> 
> Error in function (classes, fdef, mtable)  : unable to find an
> inherited method for function "indexProbes", for signature
> "AffyBatch", "list"
> 
> 
>> temp <- indexProbes(rawdata)
> 
> Error in function (classes, fdef, mtable)  : unable to find an
> inherited method for function "indexProbes", for signature
> "AffyBatch", "missing"
> 
>> sessionInfo()
> 
> R version 2.4.0 (2006-10-03) powerpc-apple-darwin8.7.0
> 
> locale: en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> 
> attached base packages: [1] "tools"     "methods"   "stats"
> "graphics"  "grDevices" [6] "utils"     "datasets"  "base"
> 
> other attached packages: made4 scatterplot3d          ade4
> affy        affyio "1.8.0"      "0.3-24"       "1.4-2"      "1.12.1"
> "1.2.0" Biobase "1.12.2"
> 
> Is this a bug?

Yeah, looks like two to me. In the overview() function of made4, there
is a call to boxplot() that includes a par(las=2), which is being passed
into indexProbes() mistakenly as the 'which' argument. The 'which'
argument is supposed to be one of ('pm', 'mm', 'both'), so indexProbes()
is burping when it sees which=par(las=2), which is a list (hence the
error about 'unable to find an inherited method for function
"indexProbes", for signature "AffyBatch", "list"'). Anyway, the
overview() function should probably read something like

opar <- par(no.readonly = TRUE)
par(las=2)
boxplot(dataset, main = paste("boxplot", title, sep = " "),
         names = labels, col = cols)
par(opar)

to protect from that happening. Aedin Culhane is the maintainer of 
made4, so I am cc'ing her.

The second error you see is because indexProbes(rawdata) is being called
without a 'which' argument. The function would set a default of 'pm'in
previous versions of R, but it appears that there is now a call to
validObject() before the default is set, so you get an error because the
indexProbes() method expects a 'which' argument that won't appear until
it gets into the body of the function. I think this part is a bug as well.

I don't know enough about S4 methods to fix this, so I am cc'ing Martin 
Morgan, who does.

Best,

Jim

> 
> Thanks, Jenny Jenny Drnevich, Ph.D. Functional Genomics
> Bioinformatics Specialist Roy J. Carver Biotechnology Center 
> University of Illinois, Urbana-Champaign
> 
> 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801
> 
> ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu
> 
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-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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