[BioC] Error coerce in AffyQCReport
Iain Gallagher
iaingallagher at btopenworld.com
Wed Dec 1 19:40:16 CET 2010
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 at fhcrc.org> wrote:
> From: Martin Morgan <mtmorgan at fhcrc.org>
> Subject: Re: [BioC] Error coerce in AffyQCReport
> To: "Lorenzo Melchor" <lorenzo.melchor at icr.ac.uk>
> Cc: bioconductor at r-project.org, "Sean Davis" <sdavis2 at mail.nih.gov>, craig.parman at bifx.org
> 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 at icr.ac.uk
>
> >>> 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 at icr.ac.uk
>
> >>> 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 at icr.ac.uk
> >>
> >>
> >>
> >>
> >>
> >> 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}}
> >
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