[Bioc-devel] SnpFeatureSet validity error in oligo

[James MacDonald]

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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