[BioC] Beadarray error: comparison of types not implemented

[Anne-Kristin Stavrum]

I am trying to use the beadarray package with some beadlevel data I 
have. The problem occurs when I try to create bead summary data :

BLData = readIllumina(arrayNames = targets$arrayID, path = "./rawdata", 
targets = targets, backgroundMethod="none", 
useImage=FALSE,annoPkg="Humanv3" )
BLData.bc = backgroundCorrect(BLData)

BSData = createBeadSummaryData(BLData.bc, imagesPerArray = 1)
Error in .nextMethod(e1, e2) :
  comparison of these types is not implemented

I see others have posted messages about this error using other packages, 
and that a possible explanation is that the objects aren't what we think 
they are.. So summary of the input object tells me that I have a 
BeadLevelList, which is what I think I should have.. so really don't get 
why this doesn't work..

 summary(BLData.bc)
       Length         Class          Mode
            1 BeadLevelList            S4

I have tried using both beadarray_1.10.0 and version 1.11.5, with R 2.8.1

I have listed sessionInfo and traceback underneath.

Does anyone have any idea about why this happens? Or what I need to do 
to get it to work?

Thanks,

Anne-Kristin Stavrum
University of Bergen, Norway


 > sessionInfo()
R version 2.8.1 (2008-12-22)
x86_64-redhat-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] tools     stats     graphics  grDevices utils     datasets  methods 
[8] base    

other attached packages:
[1] beadarray_1.11.5   sma_0.5.15         hwriter_1.1        
geneplotter_1.12.0
[5] annotate_1.12.1    Biobase_1.12.2     limma_2.9.13     

loaded via a namespace (and not attached):
[1] AnnotationDbi_1.4.3 DBI_0.2-4           KernSmooth_2.22-22
[4] RColorBrewer_0.2-3  RSQLite_0.7-1


traceback()
34: eval(expr, envir, enclos)
33: eval(call, callEnv)
32: callNextMethod(e1, e2)
31: classVersion(object)[names(vers)] == vers
30: classVersion(object)[names(vers)] == vers
29: isCurrent(object, class(object))
28: isCurrent(object, class(object))
27: isCurrent(object)
26: isCurrent(object)
25: isValidVersion(object, "eSet")
24: validMsg(msg, isValidVersion(object, "eSet"))
23: validityMethod(as(object, superClass))
22: identical(x, TRUE)
21: anyStrings(validityMethod(as(object, superClass)))
20: validObject(.Object)
19: .nextMethod(.Object, ...)
18: eval(expr, envir, enclos)
17: eval(call, callEnv)
16: callNextMethod(.Object, ...)
15: .local(.Object, ...)
14: .nextMethod(.Object, assayData = assayData, phenoData = phenoData,
        featureData = featureData, experimentData = experimentData,
        annotation = annotation)
13: eval(expr, envir, enclos)
12: eval(call, callEnv)
11: callNextMethod(.Object, assayData = assayData, phenoData = phenoData,
        featureData = featureData, experimentData = experimentData,
        annotation = annotation)
10: .local(.Object, ...)
9: .nextMethod(.Object, assayData = assayData, phenoData = phenoData,
       experimentData = experimentData, annotation = annotation,
       featureData = featureData)
8: eval(expr, envir, enclos)
7: eval(call, callEnv)
6: callNextMethod(.Object, assayData = assayData, phenoData = phenoData,
       experimentData = experimentData, annotation = annotation,
       featureData = featureData)
5: .local(.Object, ...)
4: initialize(value, ...)
3: initialize(value, ...)
2: new("ExpressionSetIllumina")
1: createBeadSummaryData(BLData.bc, imagesPerArray = 1)