1 Dec 2010 19:40
Re: Error coerce in AffyQCReport
I had this same error a couple of days ago. It was caused by simpleaffy. I ended up loading simpleaffy separately (before anything else except affy), using it's functions then unloading it (detach) and then generating various other metrics the long way. I meant to post the error but was too busy. HTH iain --- On Wed, 1/12/10, Martin Morgan <mtmorgan@...> wrote: > From: Martin Morgan <mtmorgan@...> > Subject: Re: [BioC] Error coerce in AffyQCReport > To: "Lorenzo Melchor" <lorenzo.melchor@...> > Cc: bioconductor@..., "Sean Davis" <sdavis2@...>, craig.parman@... > Date: Wednesday, 1 December, 2010, 16:51 > 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 > _______________________________________________ Bioconductor mailing list Bioconductor@... https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
RSS Feed