[BioC] arrayQualityMetrics unable to find an inherited method for function \"platformspecific\", for signature \"character\"
guest at bioconductor.org
Thu Mar 8 11:40:26 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, so would u like tell me how to fix that, appreciate very much. And i can call the arrayQualityMetrics on the MLL.A subject provided in the data package ALLMLL without any error.
-- output of sessionInfo():
R version 2.14.2 (2012-02-29)
Platform: x86_64-pc-mingw32/x64 (64-bit)
 LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
 LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
 hgu133acdf_2.9.1 ALLMLL_1.2.11 annotate_1.32.1 affyPLM_1.30.0
 preprocessCore_1.16.0 gcrma_2.26.0 affyio_1.22.0 maizecdf_2.9.1
 AnnotationDbi_1.16.18 affy_1.32.1 arrayQualityMetrics_3.10.0 Biobase_2.14.0
loaded via a namespace (and not attached):
 beadarray_2.4.1 Biostrings_2.22.0 Cairo_1.5-1 cluster_1.14.2 DBI_0.2-5
 genefilter_1.36.0 grid_2.14.2 Hmisc_3.9-2 hwriter_1.3 IRanges_1.12.6
 KernSmooth_2.23-7 lattice_0.20-0 latticeExtra_0.6-19 limma_3.10.3 RColorBrewer_1.0-5
 RSQLite_0.11.1 setRNG_2009.11-1 splines_2.14.2 survival_2.36-12 SVGAnnotation_0.9-0
 tools_2.14.2 vsn_3.22.0 XML_3.9-4.1 xtable_1.7-0 zlibbioc_1.0.1
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