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

henlen [guest] guest at bioconductor.org
Thu Mar 8 13:12:57 CET 2012

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",
                  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"

AffyBatch object
size of arrays=732x732 features (17 kb)
cdf=Maize (17734 affyids)
number of samples=1
number of genes=17734

ExpressionSet (storageMode: lockedEnvironment)
assayData: 17734 features, 1 samples 
  element names: exprs 
  sampleNames: GSM162264.CEL
  varLabels: ScanDate
  varMetadata: labelDescription
  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)

[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 

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