[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",
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
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