1 Dec 2010 17:51
Re: Error coerce in AffyQCReport
On 12/01/2010 03:51 AM, Lorenzo Melchor wrote: > Hi again, > > Sorry for the misunderstanding. > > I have repeated what you have done and got the same issue. See below: > > > library(affyQCReport) > > library(affydata) > > data(Dilution) > > QCReport(Dilution,file='qc.pdf') > Error in as.double(y) : > cannot coerce type 'S4' to vector of type 'double' The arrayQualityMetrics library might be a good alternative. Martin > > sessionInfo() > > R version 2.12.0 (2010-10-15) > Platform: i386-apple-darwin9.8.0/i386 (32-bit) > > locale: > [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] hgu95av2cdf_2.7.0 affydata_1.11.10 affyQCReport_1.28.0 > lattice_0.19-13 > [5] affy_1.28.0 Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] affyio_1.18.0 affyPLM_1.26.0 annotate_1.28.0 > [4] AnnotationDbi_1.12.0 Biostrings_2.18.2 DBI_0.2-5 > [7] gcrma_2.22.0 genefilter_1.32.0 grid_2.12.0 > [10] IRanges_1.8.0 preprocessCore_1.12.0 RColorBrewer_1.0-2 > [13] RSQLite_0.9-2 simpleaffy_2.26.0 splines_2.12.0 > [16] survival_2.35-8 tools_2.12.0 xtable_1.5-6 > > Lorenzo > > On 1 Dec 2010, at 11:40, Sean Davis wrote: > >> >> >> On Wed, Dec 1, 2010 at 6:23 AM, Lorenzo Melchor <lorenzo.melchor@... >>> wrote: >> Hi, Sean. >> >> Please, find attached one or the examples that I have tried to run. >> The problem is regardless of the samples you work with. >> >> >> Hi, Lorenzo. If I run the example for QCReport, I see the same error. >> >> Here is what I meant with reproducible example and sessionInfo(). >> >>> library(affyQCReport) >>> library(affydata) >>> data(Dilution) >>> QCReport(Dilution,file='qc.pdf') >> Error in as.double(y) : >> cannot coerce type 'S4' to vector of type 'double' >>> sessionInfo() >> R version 2.12.0 Under development (unstable) (2010-04-30 r51866) >> i386-apple-darwin9.8.0 >> >> locale: >> [1] en_US/en_US/C/C/en_US/en_US >> >> attached base packages: >> [1] stats graphics grDevices datasets utils methods base >> >> other attached packages: >> [1] hgu95av2cdf_2.7.0 affydata_1.11.10 affyQCReport_1.28.0 >> [4] lattice_0.18-8 affy_1.27.0 Biobase_2.10.0 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.17.0 affyPLM_1.26.0 annotate_1.27.0 >> [4] AnnotationDbi_1.11.9 Biostrings_2.17.8 DBI_0.2-5 >> [7] gcrma_2.22.0 genefilter_1.31.0 grid_2.12.0 >> [10] IRanges_1.7.7 preprocessCore_1.11.0 RColorBrewer_1.0-2 >> [13] RSQLite_0.9-2 simpleaffy_2.26.0 splines_2.12.0 >> [16] survival_2.35-8 tools_2.12.0 xtable_1.5-6 >> >> >> >> >> On 1 Dec 2010, at 11:17, Sean Davis wrote: >> >> >> >> On Wed, Dec 1, 2010 at 5:59 AM, Lorenzo Melchor <lorenzo.melchor@... >>> wrote: >> Hi there, >> >> I have been trying to use AffyQCReport for a few days now and I keep >> having the same problem again and again. >> >> I load the package with the usual library(affy) and >> library(affyQCReport) commands, so I type then the next command >> obtaining an error as a result. >> >> > QCReport(test,file="qualityReport.pdf") >> >> Error in as.double(y) : >> cannot coerce type 'S4' to vector of type 'double' >> >> When checking in my working directory, I find a pdf file with only the >> first two pages of any AffyQCReport. >> >> It seems odd because some other people at my centre has tried to do >> the same analysis, and got the same error. >> >> Would you know which the cause would be? >> >> >> Hi, Lorenzo. >> >> Can you give a reproducible example and sessionInfo()? >> >> Sean >> >> Lorenzo Melchor, PhD >> Mammary Stem Cell Team >> The Breakthrough Breast Cancer Research Centre (ICR) >> 237 Fulham Road >> SW3 6JB >> lorenzo.melchor@... >> >> >> >> >> >> The Institute of Cancer Research: Royal Cancer Hospital, a >> charitable Company Limited by Guarantee, Registered in England under >> Company No. 534147 with its Registered Office at 123 Old Brompton >> Road, London SW7 3RP. >> >> This e-mail message is confidential and for use by the...{{dropped:29}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor@... > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793 _______________________________________________ Bioconductor mailing list Bioconductor@... https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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