[BioC] error while using oligo to build a custom affy cdf

[James W. MacDonald]

Hi Mark,

Mark Kimpel wrote:
> I need to build a custom cdf for Affy Rat Gene ST 1.0 chipset and am
> attempting to follow Jim's helpful suggestions which can be found at
> http://article.gmane.org/gmane.science.biology.informatics.conductor/18963/match=oligo+st
> I get the error '"AffyGenePDInfoPkgSeed" is not a defined class'. My script,
> debugging info and sessionInfo is below. Any help is much appreciated.
> 
> Mark
> 
>> require(oligo)

You need to load the pdInfoBuilder package to build pdInfoPackages ;-D

Best,

Jim


> Loading required package: oligo
> Loading required package: splines
> Loading required package: RSQLite
> Loading required package: DBI
> Loading required package: preprocessCore
> Loading required package: AnnotationDbi
> Loading required package: affxparser
> Loading required package: oligoClasses
> oligo Package - Series 1.5.x
>> setwd("~/R.functions/Annotation_builds/Rat_ST_1.0_lib_files")
>> pgfFile <- "RaGene-1_0-st-v1.r3.pgf"
>> clfFile <- "MoGene-1_0-st-v1.r3.clf"
>> transFile <- "RaGene-1_0-st-v1.na26.rn4.transcript.csv"
>> probeFile <- "RaGene-1_0-st-v1.probe.tab"
>> pkg <- new("AffyGenePDInfoPkgSeed", author = "authorname", email =
> + "mwkimpel at gmail.com", version = "0.0.1", genomebuild = "July,2008",
> + biocViews = "AnnotationData", pgfFile = pgfFile, clfFile = clfFile,
> + transFile = transFile, probeFile = probeFile)
> Error in getClass(Class, where = topenv(parent.frame())) :
>   "AffyGenePDInfoPkgSeed" is not a defined class
> 
> Enter a frame number, or 0 to exit
> 
> 1: new("AffyGenePDInfoPkgSeed", author = "authorname", email =
> "mwkimpel at gmail
> 2: getClass(Class, where = topenv(parent.frame()))
> 
> Selection: 2
> Called from: eval(expr, envir, enclos)
> Browse[1]> ls()
> [1] "Class" "value" "where"
> Browse[1]> Class
> [1] "AffyGenePDInfoPkgSeed"
> Browse[1]> value
> NULL
> Browse[1]> where
> where 1: eval(expr, envir, enclos)
> where 2: eval(quote(browser()), envir = sys.frame(which))
> where 3: function ()
> {
>     if (.isMethodsDispatchOn()) {
>         tState <- tracingState(FALSE)
>         on.exit(tracingState(tState))
>     }
>     calls <- sys.calls()
>     from <- 0
>     n <- length(calls)
>     if (identical(sys.function(n), recover))
>         n <- n - 1
>     for (i in rev(seq_len(n))) {
>         calli <- calls[[i]]
>         fname <- calli[[1]]
>         if (!is.na(match(deparse(fname)[1], c("methods::.doTrace",
>             ".doTrace")))) {
>             from <- i - 1
>             break
>         }
>     }
>     if (from == 0)
>         for (i in rev(seq_len(n))) {
>             calli <- calls[[i]]
>             fname <- calli[[1]]
>             if (!is.name(fname) || is.na(match(as.character(fname),
>                 c("recover", "stop", "Stop")))) {
>                 from <- i
>                 break
>             }
>         }
>     if (from > 0) {
>         if (!interactive()) {
>             try(dump.frames())
>             cat(gettext("recover called non-interactively; frames dumped,
> use debugger() to view\n"))
>             return(NULL)
>         }
>         else if (identical(getOption("show.error.messages"),
>             FALSE))
>             return(NULL)
>         calls <- limitedLabels(calls[1:from])
>         repeat {
>             which <- menu(calls, title = "\nEnter a frame number, or 0 to
> exit  ")
>             if (which > 0)
>                 eval(quote(browser()), envir = sys.frame(which))
>             else break
>         }
>     }
>     else cat(gettext("No suitable frames for recover()\n"))
> }()
> where 4: stop(gettextf("\"%s\" is not a defined class", Class), domain = NA)
> where 5: getClass(Class, where = topenv(parent.frame()))
> where 6: new("AffyGenePDInfoPkgSeed", author = "authorname", email = "
> mwkimpel at gmail.com",
>     version = "0.0.1", genomebuild = "July,2008", biocViews =
> "AnnotationData",
>     pgfFile = pgfFile, clfFile = clfFile, transFile = transFile,
>     probeFile = probeFile)
> 
> Browse[1]> c
> 
> Enter a frame number, or 0 to exit
> 
> 1: new("AffyGenePDInfoPkgSeed", author = "authorname", email =
> "mwkimpel at gmail
> 2: getClass(Class, where = topenv(parent.frame()))
> 
> Selection: 0
>> sessionInfo()
> R version 2.8.0 Under development (unstable) (2008-08-30 r46465)
> x86_64-unknown-linux-gnu
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> [8] methods   base
> 
> other attached packages:
> [1] oligo_1.5.9          oligoClasses_1.3.6   affxparser_1.13.8
> [4] AnnotationDbi_1.3.12 preprocessCore_1.3.4 RSQLite_0.7-0
> [7] DBI_0.2-4            Biobase_2.1.7        graph_1.19.6
> 
> loaded via a namespace (and not attached):
> [1] cluster_1.11.11
> ------------------------------------------------------------
> Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
> Indiana University School of Medicine
> 
> 15032 Hunter Court, Westfield, IN  46074
> 
> (317) 490-5129 Work, & Mobile & VoiceMail
> (317) 399-1219  Home
> Skype:  mkimpel
> 
> "The real problem is not whether machines think but whether men do." -- B.
> F. Skinner
> ******************************************************************
> 

-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662