[BioC] Beadarray error: comparison of types not implemented
Martin Morgan
mtmorgan at fhcrc.org
Wed Apr 1 00:08:35 CEST 2009
Hi Anne-Kristin --
Anne-Kristin Stavrum <Anne-Kristin.Stavrum at med.uib.no> writes:
> 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?
your packages are a real mix -- beadarray 1.11.5 is from the
development branch, Biobase 1.12.2 is from several years ago, I
think. The place to start is to bring some sense to this, at least
updating installed packages as described on
http://bioconductor.org/docs/install/
but since you're using the devel. version of beadarray then perhaps
what you want is to use the devel. version of R and the devel. version
of Bioconductor packages, e.g., install the devel version of R, then
> source('http://bioconductor.org/biocLite.R')
> biocLite('beadarray')
For what it's worth it appears from the traceback that
> 2: new("ExpressionSetIllumina")
causes the problem on your system. This succeeds with the sessionInfo
as below...
> sessionInfo()
R version 2.8.1 Patched (2009-03-27 r48262)
x86_64-unknown-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_1.10.0 sma_0.5.15 hwriter_1.1
[4] geneplotter_1.20.0 annotate_1.20.1 xtable_1.5-4
[7] AnnotationDbi_1.4.2 lattice_0.17-20 Biobase_2.2.2
[10] limma_2.16.5
loaded via a namespace (and not attached):
[1] DBI_0.2-4 grid_2.8.1 KernSmooth_2.22-22 RColorBrewer_1.0-2
[5] RSQLite_0.7-1
is deep within Biobase; it could be that your object is quite
outdated; have you tried updateObject() or recreating it?
> 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)
>
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--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M2 B169
Phone: (206) 667-2793
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