[BioC] arrayQualityMetrics unable to find an inherited method for function \"platformspecific\", for signature \"character\"

[Benilton Carvalho]

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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