[BioC] arrayQualityMetrics unable to find an inherited method for function \"platformspecific\", for signature \"character\"
Benilton Carvalho
beniltoncarvalho at gmail.com
Thu Mar 8 14:05:16 CET 2012
your call is expected to be
arrayQualityMetrics(expressionset = ntest,
outdir = "Report_ntest",
force = TRUE)
note: no quotes around ntest.
b
On 8 March 2012 12:12, henlen [guest] <guest at bioconductor.org> wrote:
>
> when i running arrayQualityMetrics, i met a broblem like this,
> Error in function (classes, fdef, mtable):
> unable to find an inherited method for function "platformspecific", for signature "character".
> I want to use arrayQualityMetrics to analyse Affymetrix data- after preprocessing.
>
> Before using
> arrayQualityMetrics, i used ReadAffy on my CEL file to get an AffyBatch abject,
> then used RMA algorithm on the object to obtain a preprocessed dataset,
> finally called arrayQualityMetrics to analyse the preprocessed, then the error appeared.
>
> when called ReadAffy and rma, no erros found,
> and i can call the arrayQualityMetrics on the MLL.A subject provided in the data package ALLMLL without any error.
>
> Following is the commonds i used and the results,
> GSM162264.CEL is the CEL file got from GEO.
>
>>test <- ReadAffy("GSM162264.CEL",
> widget=getOption("BioC")$affy$use.widgets,
> celfile.path=NULL,
> sampleNames=NULL,
> phenoData=NULL,
> description=NULL,
> notes="",
> rm.mask=FALSE, rm.outliers=FALSE, rm.extra=FALSE,
> verbose=FALSE,sd=FALSE, cdfname = NULL)
>
>>ntest = rma(test)
>
>>arrayQualityMetrics(expressionset = "ntest",
> outdir = "Report_ntest",
> force = TRUE)
> The report will be written into directory 'Report_ntest'.
> Error in function (classes, fdef, mtable) :
> unable to find an inherited method for function "platformspecific", for signature "character"
>
>
>>test
> AffyBatch object
> size of arrays=732x732 features (17 kb)
> cdf=Maize (17734 affyids)
> number of samples=1
> number of genes=17734
> annotation=maize
> notes=
>
>>ntest
> ExpressionSet (storageMode: lockedEnvironment)
> assayData: 17734 features, 1 samples
> element names: exprs
> protocolData
> sampleNames: GSM162264.CEL
> varLabels: ScanDate
> varMetadata: labelDescription
> phenoData
> sampleNames: GSM162264.CEL
> varLabels: sample
> varMetadata: labelDescription
> featureData: none
> experimentData: use 'experimentData(object)'
> Annotation: maize
>
> so, how should i fix the problem, expecting for your help, appreciate very much.
>
> -- output of sessionInfo():
>
> R version 2.14.2 (2012-02-29)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] vsn_3.22.0 limma_3.10.3 hgu133acdf_2.9.1 ALLMLL_1.2.11
> [5] annotate_1.32.1 affyPLM_1.30.0 preprocessCore_1.16.0 gcrma_2.26.0
> [9] affyio_1.22.0 maizecdf_2.9.1 AnnotationDbi_1.16.18 affy_1.32.1
> [13] arrayQualityMetrics_3.10.0 Biobase_2.14.0 BiocInstaller_1.2.1
>
> loaded via a namespace (and not attached):
> [1] beadarray_2.4.1 Biostrings_2.22.0 Cairo_1.5-1 cluster_1.14.2 DBI_0.2-5
> [6] genefilter_1.36.0 grid_2.14.2 Hmisc_3.9-2 hwriter_1.3 IRanges_1.12.6
> [11] KernSmooth_2.23-7 lattice_0.20-0 latticeExtra_0.6-19 RColorBrewer_1.0-5 RSQLite_0.11.1
> [16] setRNG_2009.11-1 splines_2.14.2 survival_2.36-12 SVGAnnotation_0.9-0 tools_2.14.2
> [21] XML_3.9-4.1 xtable_1.7-0 zlibbioc_1.0.1
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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