Beadarray error: comparison of types not implemented
0
0
Entering edit mode
@martin-morgan-1513
Last seen 6 weeks ago
United States
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_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=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_IDEN TIFICATION=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) > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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
Annotation ExperimentData Cancer Biobase beadarray Annotation ExperimentData Cancer • 1.3k views
ADD COMMENT

Login before adding your answer.

Traffic: 773 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6