[Bioc-devel] SnpFeatureSet validity error in oligo

[Benilton Carvalho]

Hi Jim,

it's the pdenv... i had to put some 'fake names' in the pdenv to pass the 
validation.

i'll give you a new pdenv, ok?

thanks,

b

On Thu, 1 Jun 2006, James MacDonald wrote:

> I don't know if this is a question for Benilton or Martin Morgan (or
> someone else?). Anyway, I am getting an error when I try to create a
> SnpFeatureSet with some Affy SNP array data. Following is the code and
> error:
>
>> dat <- read.celfiles(filenames=list.celfiles())
> Incompatible phenoData object. Created a new one.
> Loading pdmapping50kxba240
> Package loaded.
> Error in if (!all(featureNames(assayData(object)) ==
> featureNames(object))) msg <- paste(msg,  :
> 	missing value where TRUE/FALSE needed
>
>
>> traceback()
> 14: validityMethod(as(object, superClass))
> 13: identical(x, TRUE)
> 12: anyStrings(validityMethod(as(object, superClass)))
> 11: validObject(.Object)
> 10: .local(.Object, ...)
> 9: .nextMethod(.Object, assayData = assayDataNew(storage.mode = "list",
>       exprs = exprs, sd = sd, npixels = npixels), phenoData =
> phenoData,
>       experimentData = experimentData, annotation = annotation)
> 8: eval(expr, envir, enclos)
> 7: eval(call, callEnv)
> 6: callNextMethod(.Object, assayData = assayDataNew(storage.mode =
> "list",
>       exprs = exprs, sd = sd, npixels = npixels), phenoData =
> phenoData,
>       experimentData = experimentData, annotation = annotation)
> 5: .local(.Object, ...)
> 4: initialize(value, ...)
> 3: initialize(value, ...)
> 2: new(TheClass, exprs = tmpExprs, sd = tmpSD, npixels = tmpNP,
>       platform = pkgname, manufacturer = "Affymetrix", phenoData =
> tmp$phenoData,
>       experimentData = tmp$description)
> 1: read.celfiles(filenames = list.celfiles())
>> sessionInfo()
> R version 2.4.0 Under development (unstable) (2006-05-01 r37954)
> x86_64-unknown-linux-gnu
>
> attached base packages:
> [1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
>
> [7] "datasets"  "base"
>
> other attached packages:
> pdmapping50kxba240              oligo             affyio
> Biobase
>           "0.5.0"          "0.99.10"            "1.1.0"
> "1.11.12"
>
> Any takers?
>
> Best,
>
> Jim
>
>
>
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
>
>
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