error with makecdfenv package
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@james-w-macdonald-5106
Last seen 5 hours ago
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Hi Trang Tran, I am redirecting this to the bioconductor help list, so others may benefit as well. On 7/16/2014 10:22 AM, TRAN Trang wrote: > Dear all, > > I?m using the makecdfenv package to creat a annotation package for the > chip Affymetrix HTA 2.0 from .CDF file but I get the following error: You won't be able to use the makecdfenv/affy pipeline for this array. That pipeline is intended for the old 3'-biased arrays. The HTA arrays are very complex, being intended to measure transcript splice variants. The pdInfoBuilder/oligo pipeline will allow you to read in and summarize the data. I don't know about the xps package, but perhaps Christian Stratowa will respond. Although you can summarize the data using oligo, there aren't (to my knowledge) any packages in BioC that are intended to analyze these data. Note that for each gene there are any number of probesets that are intended to measure either exon abundance or to measure the existence of an exon-exon junction. Summarizing those data into a measure (or measures) that can be used to infer differential transcript splicing is probably not a trivial exercise. I would be interested to hear if anybody is trying to develop a package for the analysis of these arrays. Best, Jim > > Reading CDF file. > > Creating CDF environment > > Wait for about 681 > > Creating package in C:/DATA/mes documents/htagene > > Erreur dans copySubstitute(dir(originDir, full.names = TRUE), pkgdir, > symbolValues, : > > 'symbolValues' must only contain characters. > > Could you please let me know how can fit it? > > Thank you in advance! > > Best regards, > > Trang Tran >
Annotation cdf makecdfenv oligo xps Annotation cdf makecdfenv oligo xps • 1.5k views
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cstrato ★ 3.9k
@cstrato-908
Last seen 5.5 years ago
Austria
Dear Jim, Please see my response from March: https://stat.ethz.ch/pipermail/bioconductor/2014-March/058538.html Best regards, Christian On 7/16/14 7:03 PM, James W. MacDonald wrote: > Hi Trang Tran, > > I am redirecting this to the bioconductor help list, so others may > benefit as well. > > On 7/16/2014 10:22 AM, TRAN Trang wrote: >> Dear all, >> >> I?m using the makecdfenv package to creat a annotation package for the >> chip Affymetrix HTA 2.0 from .CDF file but I get the following error: > > You won't be able to use the makecdfenv/affy pipeline for this array. > That pipeline is intended for the old 3'-biased arrays. > > The HTA arrays are very complex, being intended to measure transcript > splice variants. The pdInfoBuilder/oligo pipeline will allow you to read > in and summarize the data. I don't know about the xps package, but > perhaps Christian Stratowa will respond. > > Although you can summarize the data using oligo, there aren't (to my > knowledge) any packages in BioC that are intended to analyze these data. > Note that for each gene there are any number of probesets that are > intended to measure either exon abundance or to measure the existence of > an exon-exon junction. > > Summarizing those data into a measure (or measures) that can be used to > infer differential transcript splicing is probably not a trivial > exercise. I would be interested to hear if anybody is trying to develop > a package for the analysis of these arrays. > > Best, > > Jim > > >> >> Reading CDF file. >> >> Creating CDF environment >> >> Wait for about 681 >> >> Creating package in C:/DATA/mes documents/htagene >> >> Erreur dans copySubstitute(dir(originDir, full.names = TRUE), pkgdir, >> symbolValues, : >> >> 'symbolValues' must only contain characters. >> >> Could you please let me know how can fit it? >> >> Thank you in advance! >> >> Best regards, >> >> Trang Tran >> > > _______________________________________________ > 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 >
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Hi Christian, Thanks! Are there any plans to support these arrays in future, or should I assume that pdInfoBuilder/oligo are the only way to go? Best, Jim On 7/16/2014 1:39 PM, cstrato wrote: > Dear Jim, > > Please see my response from March: > https://stat.ethz.ch/pipermail/bioconductor/2014-March/058538.html > > Best regards, > Christian > > > On 7/16/14 7:03 PM, James W. MacDonald wrote: >> Hi Trang Tran, >> >> I am redirecting this to the bioconductor help list, so others may >> benefit as well. >> >> On 7/16/2014 10:22 AM, TRAN Trang wrote: >>> Dear all, >>> >>> I?m using the makecdfenv package to creat a annotation package for the >>> chip Affymetrix HTA 2.0 from .CDF file but I get the following error: >> >> You won't be able to use the makecdfenv/affy pipeline for this array. >> That pipeline is intended for the old 3'-biased arrays. >> >> The HTA arrays are very complex, being intended to measure transcript >> splice variants. The pdInfoBuilder/oligo pipeline will allow you to read >> in and summarize the data. I don't know about the xps package, but >> perhaps Christian Stratowa will respond. >> >> Although you can summarize the data using oligo, there aren't (to my >> knowledge) any packages in BioC that are intended to analyze these data. >> Note that for each gene there are any number of probesets that are >> intended to measure either exon abundance or to measure the existence of >> an exon-exon junction. >> >> Summarizing those data into a measure (or measures) that can be used to >> infer differential transcript splicing is probably not a trivial >> exercise. I would be interested to hear if anybody is trying to develop >> a package for the analysis of these arrays. >> >> Best, >> >> Jim >> >> >>> >>> Reading CDF file. >>> >>> Creating CDF environment >>> >>> Wait for about 681 >>> >>> Creating package in C:/DATA/mes documents/htagene >>> >>> Erreur dans copySubstitute(dir(originDir, full.names = TRUE), pkgdir, >>> symbolValues, : >>> >>> 'symbolValues' must only contain characters. >>> >>> Could you please let me know how can fit it? >>> >>> Thank you in advance! >>> >>> Best regards, >>> >>> Trang Tran >>> >> >> _______________________________________________ >> 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 >>
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Dear Jim, I do not have any plans to support these arrays in the future so oligo would be the only way to go. Best regards, Christian On 7/16/14 7:49 PM, James W. MacDonald wrote: > Hi Christian, > > Thanks! Are there any plans to support these arrays in future, or should > I assume that pdInfoBuilder/oligo are the only way to go? > > Best, > > Jim > > > > On 7/16/2014 1:39 PM, cstrato wrote: >> Dear Jim, >> >> Please see my response from March: >> https://stat.ethz.ch/pipermail/bioconductor/2014-March/058538.html >> >> Best regards, >> Christian >> >> >> On 7/16/14 7:03 PM, James W. MacDonald wrote: >>> Hi Trang Tran, >>> >>> I am redirecting this to the bioconductor help list, so others may >>> benefit as well. >>> >>> On 7/16/2014 10:22 AM, TRAN Trang wrote: >>>> Dear all, >>>> >>>> I?m using the makecdfenv package to creat a annotation package for the >>>> chip Affymetrix HTA 2.0 from .CDF file but I get the following error: >>> >>> You won't be able to use the makecdfenv/affy pipeline for this array. >>> That pipeline is intended for the old 3'-biased arrays. >>> >>> The HTA arrays are very complex, being intended to measure transcript >>> splice variants. The pdInfoBuilder/oligo pipeline will allow you to read >>> in and summarize the data. I don't know about the xps package, but >>> perhaps Christian Stratowa will respond. >>> >>> Although you can summarize the data using oligo, there aren't (to my >>> knowledge) any packages in BioC that are intended to analyze these data. >>> Note that for each gene there are any number of probesets that are >>> intended to measure either exon abundance or to measure the existence of >>> an exon-exon junction. >>> >>> Summarizing those data into a measure (or measures) that can be used to >>> infer differential transcript splicing is probably not a trivial >>> exercise. I would be interested to hear if anybody is trying to develop >>> a package for the analysis of these arrays. >>> >>> Best, >>> >>> Jim >>> >>> >>>> >>>> Reading CDF file. >>>> >>>> Creating CDF environment >>>> >>>> Wait for about 681 >>>> >>>> Creating package in C:/DATA/mes documents/htagene >>>> >>>> Erreur dans copySubstitute(dir(originDir, full.names = TRUE), pkgdir, >>>> symbolValues, : >>>> >>>> 'symbolValues' must only contain characters. >>>> >>>> Could you please let me know how can fit it? >>>> >>>> Thank you in advance! >>>> >>>> Best regards, >>>> >>>> Trang Tran >>>> >>> >>> _______________________________________________ >>> 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 >>> >
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Dear all, Thank you very much for your suggestion. I tried the pdInfoBuilder/oligo, it runs very well. Best, Trang -----Message d'origine----- De?: cstrato [mailto:cstrato at aon.at] Envoy??: mercredi 16 juillet 2014 20:07 ??: James W. MacDonald; TRAN Trang Cc?: 'bioconductor at r-project.org' Objet?: Re: [BioC] error with makecdfenv package Dear Jim, I do not have any plans to support these arrays in the future so oligo would be the only way to go. Best regards, Christian On 7/16/14 7:49 PM, James W. MacDonald wrote: > Hi Christian, > > Thanks! Are there any plans to support these arrays in future, or > should I assume that pdInfoBuilder/oligo are the only way to go? > > Best, > > Jim > > > > On 7/16/2014 1:39 PM, cstrato wrote: >> Dear Jim, >> >> Please see my response from March: >> https://stat.ethz.ch/pipermail/bioconductor/2014-March/058538.html >> >> Best regards, >> Christian >> >> >> On 7/16/14 7:03 PM, James W. MacDonald wrote: >>> Hi Trang Tran, >>> >>> I am redirecting this to the bioconductor help list, so others may >>> benefit as well. >>> >>> On 7/16/2014 10:22 AM, TRAN Trang wrote: >>>> Dear all, >>>> >>>> I'm using the makecdfenv package to creat a annotation package for >>>> the chip Affymetrix HTA 2.0 from .CDF file but I get the following error: >>> >>> You won't be able to use the makecdfenv/affy pipeline for this array. >>> That pipeline is intended for the old 3'-biased arrays. >>> >>> The HTA arrays are very complex, being intended to measure >>> transcript splice variants. The pdInfoBuilder/oligo pipeline will >>> allow you to read in and summarize the data. I don't know about the >>> xps package, but perhaps Christian Stratowa will respond. >>> >>> Although you can summarize the data using oligo, there aren't (to my >>> knowledge) any packages in BioC that are intended to analyze these data. >>> Note that for each gene there are any number of probesets that are >>> intended to measure either exon abundance or to measure the >>> existence of an exon-exon junction. >>> >>> Summarizing those data into a measure (or measures) that can be used >>> to infer differential transcript splicing is probably not a trivial >>> exercise. I would be interested to hear if anybody is trying to >>> develop a package for the analysis of these arrays. >>> >>> Best, >>> >>> Jim >>> >>> >>>> >>>> Reading CDF file. >>>> >>>> Creating CDF environment >>>> >>>> Wait for about 681 >>>> >>>> Creating package in C:/DATA/mes documents/htagene >>>> >>>> Erreur dans copySubstitute(dir(originDir, full.names = TRUE), >>>> pkgdir, symbolValues, : >>>> >>>> 'symbolValues' must only contain characters. >>>> >>>> Could you please let me know how can fit it? >>>> >>>> Thank you in advance! >>>> >>>> Best regards, >>>> >>>> Trang Tran >>>> >>> >>> _______________________________________________ >>> 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 >>> >
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