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?
Thanks,
Lorenzo
Lorenzo Melchor, PhD
Mammary Stem Cell Team
The Breakthrough Breast Cancer Research Centre (ICR)
237 Fulham Road
SW3 6JB
lorenzo.melchor@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
a...{{dropped:4}}
On Wed, Dec 1, 2010 at 5:59 AM, Lorenzo Melchor
<lorenzo.melchor@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
[[alternative HTML version deleted]]
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.
Thanks,
Lorenzo
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 addressee only.
If the message is received by anyone other than the addressee, please
return the message to the sender by replying to it and then delete the
message from your computer and network.
On Wed, Dec 1, 2010 at 6:23 AM, Lorenzo Melchor
<lorenzo.melchor@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@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@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 addressee
only. If
> the message is received by anyone other than the addressee, please
return
> the message to the sender by replying to it and then delete the
message from
> your computer and network.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
[[alternative HTML version deleted]]
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'
> 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@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@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@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}}
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}}
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> 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
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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Martin Morgan <mtmorgan at="" ...=""> writes:
>
> 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'
>
I am having this exact same problem regardless of dataset.
I've been using affyQCReport for years and
this is the first time I'm come across it.
Could it be related to the mac platform?
This is the first time
I've tried to run using 64-bit mac version of R.
The linux 64-bit version of R generates the qc plots fine.
Alexander Yu
Bioinformatics Programmer
Texas Children?s Cancer Center
Alexander,
It is not a problem related to MAC apparently, as we have the same
problem in a windows platform too.
Lorenzo
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
a...{{dropped:2}}
This has been addressed in affyQCReport v. 1.28.1 / simpleaffy v.
2.26.1. These will likely be available with biocLite (under R-2.12) on
Friday (Seattle time)
source("http://bioconductor.org/biocLite.R")
biocLite(c("simpleaffy", "affyQCReport"))
Martin
----- Original Message -----
From: "Lorenzo Melchor" <lorenzo.melchor@icr.ac.uk>
To: axyu at txccc.org
Cc: Bioconductor at r-project.org
Sent: Thursday, December 2, 2010 3:13:53 AM
Subject: Re: [BioC] Error coerce in AffyQCReport
Alexander,
It is not a problem related to MAC apparently, as we have the same
problem in a windows platform too.
Lorenzo
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
a...{{dropped:8}}
