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? 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

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 > > _______________________________________________ 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 -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

...and indexProbes now handles a missing 'which' correctly. The update should appear in the repository in the next 24 hours; look for affy version 1.12.2 "James W. MacDonald" <jmacdon at="" med.umich.edu=""> writes: > Hi Jenny, > > drnevich at uiuc.edu wrote: >>> temp <- indexProbes(rawdata) >> Error in function (classes, fdef, mtable) : unable to find an >> inherited method for function "indexProbes", for signature >> "AffyBatch", "missing" > 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 For the technically minded, "indexProbes" is a so-called 'generic' function. Generic functions have 'methods' associated with them. When a user invokes a generic function, R looks at the arguments the user provides, and tries to find a method that matches those arguments. The methods available for "indexProbes" in the previous version of affy were > showMethods("indexProbes") Function: indexProbes (package affy) object="AffyBatch", which="character" i.e., R knew how to deal with a call to indexProbes when the 'object' argument was an "AffyBatch", and the 'which' argument was a "character". R did not know how to deal with a call where 'which' was missing. I added another method, so the new version of affy has > showMethods("indexProbes") Function: indexProbes (package affy) object="AffyBatch", which="character" object="AffyBatch", which="missing" This means that 'which' can be "missing". In the method, I repeat the call to indexProbes, but supply a default argument for 'which' as the character vector "pm". Martin -- Martin T. Morgan Bioconductor / Computational Biology http://bioconductor.org