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[Bioc-devel] SnpFeatureSet validity error in oligo

4 messages · James W. MacDonald, Benilton Carvalho, Martin Morgan +1 more

Original
James W. 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:
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
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())
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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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:

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      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:

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Seth Falcon
    

    

      
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Benilton Carvalho <bcarvalh at jhsph.edu> writes:

            

      
      
      
    

        
It would be great to have some further discussion of your needs for
SnpFeatureSet.  Putting in fake names seems like an unpleasant
solution.