[Bioc-devel] SnpFeatureSet validity error in oligo

[Martin Morgan]

I have partly corrected this in Biobase.

The check was non-sensical (featureNames(assayData(object)) and
featureNames(object) return the same thing). There is now a better
check to ensure that all assayData elements have the same featureNames
(rownames).

This doesn't really help, though, with the error. I think
featureNames(object) is returning 'NA', perhaps assigned during
read.celfiles in oligo.

Martin



"James MacDonald" <jmacdon at med.umich.edu> writes:

> 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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