Question: Error coerce in AffyQCReport
0
gravatar for Lorenzo Melchor
9.0 years ago by
Lorenzo Melchor50 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? 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}}
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ADD COMMENTlink modified 8.9 years ago • written 9.0 years ago by Lorenzo Melchor50
Answer: Error coerce in AffyQCReport
0
gravatar for Sean Davis
9.0 years ago by
Sean Davis21k
United States
Sean Davis21k 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 [[alternative HTML version deleted]]
ADD COMMENTlink written 9.0 years ago by Sean Davis21k
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.
ADD REPLYlink written 9.0 years ago by Lorenzo Melchor50
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]]
ADD REPLYlink written 9.0 years ago by Sean Davis21k
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}}
ADD REPLYlink written 9.0 years ago by Lorenzo Melchor50
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
ADD REPLYlink written 9.0 years ago by Martin Morgan ♦♦ 24k
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}} > > > > _______________________________________________ > > 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 > > _______________________________________________ > 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 >
ADD REPLYlink written 9.0 years ago by Iain Gallagher930
Answer: Error coerce in AffyQCReport
0
gravatar for Alexander Yu
9.0 years ago by
Alexander Yu10
Alexander Yu10 wrote:
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
ADD COMMENTlink written 9.0 years ago by Alexander Yu10
Answer: Error coerce in AffyQCReport
0
gravatar for Lorenzo Melchor
8.9 years ago by
Lorenzo Melchor50 wrote:
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}}
ADD COMMENTlink written 8.9 years ago by Lorenzo Melchor50
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}}
ADD REPLYlink written 9.0 years ago by Martin Morgan ♦♦ 24k
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