Bioconductor - hugene10stv1cdf not available
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@christoph-knapp-4029
Last seen 9.6 years ago
Hi all, I'm trying for quite some time to get an analysis started. I keep getting this Error. Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain HuGene-1_0-st-v1 Library - package hugene10stv1cdf not installed Bioconductor - hugene10stv1cdf not available Calls: rma ... .local -> indexProbes -> indexProbes -> .local -> getCdfInfo Execution halted I installed all possible packages from there http://www.bioconductor.org/docs/workflows/oligoarrays/ and even downloaded and installed that one http://mbi00206.bio.med.uni-muenchen.de/free/pd.hugene.1.0.st.v1.zip) still no change. What am I missing? It reads in the CEL files VFdata=ReadAffy() but when I look at the VFdata object it already says > VFdata AffyBatch object size of arrays=1050x1050 features (11 kb) cdf=HuGene-1_0-st-v1 (??? affyids) number of samples=7 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain HuGene-1_0-st-v1 Library - package hugene10stv1cdf not installed Bioconductor - hugene10stv1cdf not available In addition: Warning message: missing cdf environment! in show(AffyBatch) and going on > eset = exprs(rma(VFdata)) Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain HuGene-1_0-st-v1 Library - package hugene10stv1cdf not installed Bioconductor - hugene10stv1cdf not available Error in exprs(rma(VFdata)) : error in evaluating the argument 'object' in selecting a method for function 'exprs' > I'm very inexperienced in terms of stuff like that. A answer for dummies would be much appreciated. Thanks Christoph
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@benilton-carvalho-1375
Last seen 4.0 years ago
Brazil/Campinas/UNICAMP
the pd.hugene package (which I'd expect you to download from BioC) is to be used with the oligo package. b On Sun, Apr 18, 2010 at 11:51 PM, Christoph Knapp <mkna005 at="" aucklanduni.ac.nz=""> wrote: > Hi all, > I'm trying for quite some time to get an analysis started. I keep > getting this Error. > > Error in getCdfInfo(object) : > ?Could not obtain CDF environment, problems encountered: > Specified environment does not contain HuGene-1_0-st-v1 > Library - package hugene10stv1cdf not installed > Bioconductor - hugene10stv1cdf not available > Calls: rma ... .local -> indexProbes -> indexProbes -> .local -> getCdfInfo > Execution halted > > I installed all possible packages from there > > http://www.bioconductor.org/docs/workflows/oligoarrays/ > > and even downloaded and installed that one > > http://mbi00206.bio.med.uni- muenchen.de/free/pd.hugene.1.0.st.v1.zip) > > still no change. > > What am I missing? > > It reads in the CEL files > > VFdata=ReadAffy() > > but when I look at the VFdata object it already says > >> VFdata > AffyBatch object > size of arrays=1050x1050 features (11 kb) > cdf=HuGene-1_0-st-v1 (??? affyids) > number of samples=7 > Error in getCdfInfo(object) : > ?Could not obtain CDF environment, problems encountered: > Specified environment does not contain HuGene-1_0-st-v1 > Library - package hugene10stv1cdf not installed > Bioconductor - hugene10stv1cdf not available > In addition: Warning message: > missing cdf environment! in show(AffyBatch) > > and going on > >> eset = exprs(rma(VFdata)) > Error in getCdfInfo(object) : > ?Could not obtain CDF environment, problems encountered: > Specified environment does not contain HuGene-1_0-st-v1 > Library - package hugene10stv1cdf not installed > Bioconductor - hugene10stv1cdf not available > Error in exprs(rma(VFdata)) : > ?error in evaluating the argument 'object' in selecting a method for > function 'exprs' >> > > I'm very inexperienced in terms of stuff like that. A answer for > dummies would be much appreciated. > > Thanks > > Christoph > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Sorry, still no change AffyBatch object size of arrays=1050x1050 features (11 kb) cdf=HuGene-1_0-st-v1 (??? affyids) number of samples=7 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain HuGene-1_0-st-v1 Library - package hugene10stv1cdf not installed Bioconductor - hugene10stv1cdf not available In addition: Warning message: missing cdf environment! in show(AffyBatch) Christoph On 19 April 2010 11:51, Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> wrote: > the pd.hugene package (which I'd expect you to download from BioC) is > to be used with the oligo package. > > b > > On Sun, Apr 18, 2010 at 11:51 PM, Christoph Knapp > <mkna005 at="" aucklanduni.ac.nz=""> wrote: >> Hi all, >> I'm trying for quite some time to get an analysis started. I keep >> getting this Error. >> >> Error in getCdfInfo(object) : >> ?Could not obtain CDF environment, problems encountered: >> Specified environment does not contain HuGene-1_0-st-v1 >> Library - package hugene10stv1cdf not installed >> Bioconductor - hugene10stv1cdf not available >> Calls: rma ... .local -> indexProbes -> indexProbes -> .local -> getCdfInfo >> Execution halted >> >> I installed all possible packages from there >> >> http://www.bioconductor.org/docs/workflows/oligoarrays/ >> >> and even downloaded and installed that one >> >> http://mbi00206.bio.med.uni- muenchen.de/free/pd.hugene.1.0.st.v1.zip) >> >> still no change. >> >> What am I missing? >> >> It reads in the CEL files >> >> VFdata=ReadAffy() >> >> but when I look at the VFdata object it already says >> >>> VFdata >> AffyBatch object >> size of arrays=1050x1050 features (11 kb) >> cdf=HuGene-1_0-st-v1 (??? affyids) >> number of samples=7 >> Error in getCdfInfo(object) : >> ?Could not obtain CDF environment, problems encountered: >> Specified environment does not contain HuGene-1_0-st-v1 >> Library - package hugene10stv1cdf not installed >> Bioconductor - hugene10stv1cdf not available >> In addition: Warning message: >> missing cdf environment! in show(AffyBatch) >> >> and going on >> >>> eset = exprs(rma(VFdata)) >> Error in getCdfInfo(object) : >> ?Could not obtain CDF environment, problems encountered: >> Specified environment does not contain HuGene-1_0-st-v1 >> Library - package hugene10stv1cdf not installed >> Bioconductor - hugene10stv1cdf not available >> Error in exprs(rma(VFdata)) : >> ?error in evaluating the argument 'object' in selecting a method for >> function 'exprs' >>> >> >> I'm very inexperienced in terms of stuff like that. A answer for >> dummies would be much appreciated. >> >> Thanks >> >> Christoph >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >
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I forgot to mention that I tried that as well: > biocLite("hugene10stv1cdf") Using R version 2.10.1, biocinstall version 2.5.10. Installing Bioconductor version 2.5 packages: [1] "hugene10stv1cdf" Please wait... Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ?hugene10stv1cdf? is not available Why is it not possible for me to install that package. Thanks Christoph On 19 April 2010 12:13, Christoph Knapp <mkna005 at="" aucklanduni.ac.nz=""> wrote: > Sorry, > still no change > > AffyBatch object > size of arrays=1050x1050 features (11 kb) > cdf=HuGene-1_0-st-v1 (??? affyids) > number of samples=7 > Error in getCdfInfo(object) : > ?Could not obtain CDF environment, problems encountered: > Specified environment does not contain HuGene-1_0-st-v1 > Library - package hugene10stv1cdf not installed > Bioconductor - hugene10stv1cdf not available > In addition: Warning message: > missing cdf environment! in show(AffyBatch) > > Christoph > > On 19 April 2010 11:51, Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> wrote: >> the pd.hugene package (which I'd expect you to download from BioC) is >> to be used with the oligo package. >> >> b >> >> On Sun, Apr 18, 2010 at 11:51 PM, Christoph Knapp >> <mkna005 at="" aucklanduni.ac.nz=""> wrote: >>> Hi all, >>> I'm trying for quite some time to get an analysis started. I keep >>> getting this Error. >>> >>> Error in getCdfInfo(object) : >>> ?Could not obtain CDF environment, problems encountered: >>> Specified environment does not contain HuGene-1_0-st-v1 >>> Library - package hugene10stv1cdf not installed >>> Bioconductor - hugene10stv1cdf not available >>> Calls: rma ... .local -> indexProbes -> indexProbes -> .local -> getCdfInfo >>> Execution halted >>> >>> I installed all possible packages from there >>> >>> http://www.bioconductor.org/docs/workflows/oligoarrays/ >>> >>> and even downloaded and installed that one >>> >>> http://mbi00206.bio.med.uni- muenchen.de/free/pd.hugene.1.0.st.v1.zip) >>> >>> still no change. >>> >>> What am I missing? >>> >>> It reads in the CEL files >>> >>> VFdata=ReadAffy() >>> >>> but when I look at the VFdata object it already says >>> >>>> VFdata >>> AffyBatch object >>> size of arrays=1050x1050 features (11 kb) >>> cdf=HuGene-1_0-st-v1 (??? affyids) >>> number of samples=7 >>> Error in getCdfInfo(object) : >>> ?Could not obtain CDF environment, problems encountered: >>> Specified environment does not contain HuGene-1_0-st-v1 >>> Library - package hugene10stv1cdf not installed >>> Bioconductor - hugene10stv1cdf not available >>> In addition: Warning message: >>> missing cdf environment! in show(AffyBatch) >>> >>> and going on >>> >>>> eset = exprs(rma(VFdata)) >>> Error in getCdfInfo(object) : >>> ?Could not obtain CDF environment, problems encountered: >>> Specified environment does not contain HuGene-1_0-st-v1 >>> Library - package hugene10stv1cdf not installed >>> Bioconductor - hugene10stv1cdf not available >>> Error in exprs(rma(VFdata)) : >>> ?error in evaluating the argument 'object' in selecting a method for >>> function 'exprs' >>>> >>> >>> I'm very inexperienced in terms of stuff like that. A answer for >>> dummies would be much appreciated. >>> >>> Thanks >>> >>> Christoph >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >
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Hi Christoph, the way to do this with oligo is: library(oligo) rawData = read.celfiles(list.celfiles()) summaries1 = rma(rawData, target="probeset") summaries2 = rma(rawData, target="core") summaries1 will contain the rma summaries to the probeset defined in the PGF file. summaries2 will contain the summaries for the metaprobesets defined in the core.mps file. AffyBatch objects are to be used with the affy package, so that's why the pd.hugene package was of no use (b/c pd.hugene is to be used with oligo). hth, b On Mon, Apr 19, 2010 at 1:33 AM, Christoph Knapp <mkna005 at="" aucklanduni.ac.nz=""> wrote: > I forgot to mention that I tried that as well: > >> ? ? biocLite("hugene10stv1cdf") > Using R version 2.10.1, biocinstall version 2.5.10. > Installing Bioconductor version 2.5 packages: > [1] "hugene10stv1cdf" > Please wait... > > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > ?package ?hugene10stv1cdf? is not available > > Why is it not possible for me to install that package. > > Thanks > > Christoph > > On 19 April 2010 12:13, Christoph Knapp <mkna005 at="" aucklanduni.ac.nz=""> wrote: >> Sorry, >> still no change >> >> AffyBatch object >> size of arrays=1050x1050 features (11 kb) >> cdf=HuGene-1_0-st-v1 (??? affyids) >> number of samples=7 >> Error in getCdfInfo(object) : >> ?Could not obtain CDF environment, problems encountered: >> Specified environment does not contain HuGene-1_0-st-v1 >> Library - package hugene10stv1cdf not installed >> Bioconductor - hugene10stv1cdf not available >> In addition: Warning message: >> missing cdf environment! in show(AffyBatch) >> >> Christoph >> >> On 19 April 2010 11:51, Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> wrote: >>> the pd.hugene package (which I'd expect you to download from BioC) is >>> to be used with the oligo package. >>> >>> b >>> >>> On Sun, Apr 18, 2010 at 11:51 PM, Christoph Knapp >>> <mkna005 at="" aucklanduni.ac.nz=""> wrote: >>>> Hi all, >>>> I'm trying for quite some time to get an analysis started. I keep >>>> getting this Error. >>>> >>>> Error in getCdfInfo(object) : >>>> ?Could not obtain CDF environment, problems encountered: >>>> Specified environment does not contain HuGene-1_0-st-v1 >>>> Library - package hugene10stv1cdf not installed >>>> Bioconductor - hugene10stv1cdf not available >>>> Calls: rma ... .local -> indexProbes -> indexProbes -> .local -> getCdfInfo >>>> Execution halted >>>> >>>> I installed all possible packages from there >>>> >>>> http://www.bioconductor.org/docs/workflows/oligoarrays/ >>>> >>>> and even downloaded and installed that one >>>> >>>> http://mbi00206.bio.med.uni- muenchen.de/free/pd.hugene.1.0.st.v1.zip) >>>> >>>> still no change. >>>> >>>> What am I missing? >>>> >>>> It reads in the CEL files >>>> >>>> VFdata=ReadAffy() >>>> >>>> but when I look at the VFdata object it already says >>>> >>>>> VFdata >>>> AffyBatch object >>>> size of arrays=1050x1050 features (11 kb) >>>> cdf=HuGene-1_0-st-v1 (??? affyids) >>>> number of samples=7 >>>> Error in getCdfInfo(object) : >>>> ?Could not obtain CDF environment, problems encountered: >>>> Specified environment does not contain HuGene-1_0-st-v1 >>>> Library - package hugene10stv1cdf not installed >>>> Bioconductor - hugene10stv1cdf not available >>>> In addition: Warning message: >>>> missing cdf environment! in show(AffyBatch) >>>> >>>> and going on >>>> >>>>> eset = exprs(rma(VFdata)) >>>> Error in getCdfInfo(object) : >>>> ?Could not obtain CDF environment, problems encountered: >>>> Specified environment does not contain HuGene-1_0-st-v1 >>>> Library - package hugene10stv1cdf not installed >>>> Bioconductor - hugene10stv1cdf not available >>>> Error in exprs(rma(VFdata)) : >>>> ?error in evaluating the argument 'object' in selecting a method for >>>> function 'exprs' >>>>> >>>> >>>> I'm very inexperienced in terms of stuff like that. A answer for >>>> dummies would be much appreciated. >>>> >>>> Thanks >>>> >>>> Christoph >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >> >
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btw, if you want to use the affy package, I believe that the package: http://www.bioconductor.org/packages/release/data/annotation/html/huge ne10stv1.r3cdf.html should suffice (you will need to specify the name of the package to be used though, check the docs for ReadAffy). b On Mon, Apr 19, 2010 at 1:48 AM, Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> wrote: > Hi Christoph, > > the way to do this with oligo is: > > library(oligo) > rawData = read.celfiles(list.celfiles()) > summaries1 = rma(rawData, target="probeset") > summaries2 = rma(rawData, target="core") > > summaries1 will contain the rma summaries to the probeset defined in > the PGF file. summaries2 will contain the summaries for the > metaprobesets defined in the core.mps file. > > AffyBatch objects are to be used with the affy package, so that's why > the pd.hugene package was of no use (b/c pd.hugene is to be used with > oligo). > > hth, > b > > On Mon, Apr 19, 2010 at 1:33 AM, Christoph Knapp > <mkna005 at="" aucklanduni.ac.nz=""> wrote: >> I forgot to mention that I tried that as well: >> >>> ? ? biocLite("hugene10stv1cdf") >> Using R version 2.10.1, biocinstall version 2.5.10. >> Installing Bioconductor version 2.5 packages: >> [1] "hugene10stv1cdf" >> Please wait... >> >> Warning message: >> In getDependencies(pkgs, dependencies, available, lib) : >> ?package ?hugene10stv1cdf? is not available >> >> Why is it not possible for me to install that package. >> >> Thanks >> >> Christoph >> >> On 19 April 2010 12:13, Christoph Knapp <mkna005 at="" aucklanduni.ac.nz=""> wrote: >>> Sorry, >>> still no change >>> >>> AffyBatch object >>> size of arrays=1050x1050 features (11 kb) >>> cdf=HuGene-1_0-st-v1 (??? affyids) >>> number of samples=7 >>> Error in getCdfInfo(object) : >>> ?Could not obtain CDF environment, problems encountered: >>> Specified environment does not contain HuGene-1_0-st-v1 >>> Library - package hugene10stv1cdf not installed >>> Bioconductor - hugene10stv1cdf not available >>> In addition: Warning message: >>> missing cdf environment! in show(AffyBatch) >>> >>> Christoph >>> >>> On 19 April 2010 11:51, Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> wrote: >>>> the pd.hugene package (which I'd expect you to download from BioC) is >>>> to be used with the oligo package. >>>> >>>> b >>>> >>>> On Sun, Apr 18, 2010 at 11:51 PM, Christoph Knapp >>>> <mkna005 at="" aucklanduni.ac.nz=""> wrote: >>>>> Hi all, >>>>> I'm trying for quite some time to get an analysis started. I keep >>>>> getting this Error. >>>>> >>>>> Error in getCdfInfo(object) : >>>>> ?Could not obtain CDF environment, problems encountered: >>>>> Specified environment does not contain HuGene-1_0-st-v1 >>>>> Library - package hugene10stv1cdf not installed >>>>> Bioconductor - hugene10stv1cdf not available >>>>> Calls: rma ... .local -> indexProbes -> indexProbes -> .local -> getCdfInfo >>>>> Execution halted >>>>> >>>>> I installed all possible packages from there >>>>> >>>>> http://www.bioconductor.org/docs/workflows/oligoarrays/ >>>>> >>>>> and even downloaded and installed that one >>>>> >>>>> http://mbi00206.bio.med.uni- muenchen.de/free/pd.hugene.1.0.st.v1.zip) >>>>> >>>>> still no change. >>>>> >>>>> What am I missing? >>>>> >>>>> It reads in the CEL files >>>>> >>>>> VFdata=ReadAffy() >>>>> >>>>> but when I look at the VFdata object it already says >>>>> >>>>>> VFdata >>>>> AffyBatch object >>>>> size of arrays=1050x1050 features (11 kb) >>>>> cdf=HuGene-1_0-st-v1 (??? affyids) >>>>> number of samples=7 >>>>> Error in getCdfInfo(object) : >>>>> ?Could not obtain CDF environment, problems encountered: >>>>> Specified environment does not contain HuGene-1_0-st-v1 >>>>> Library - package hugene10stv1cdf not installed >>>>> Bioconductor - hugene10stv1cdf not available >>>>> In addition: Warning message: >>>>> missing cdf environment! in show(AffyBatch) >>>>> >>>>> and going on >>>>> >>>>>> eset = exprs(rma(VFdata)) >>>>> Error in getCdfInfo(object) : >>>>> ?Could not obtain CDF environment, problems encountered: >>>>> Specified environment does not contain HuGene-1_0-st-v1 >>>>> Library - package hugene10stv1cdf not installed >>>>> Bioconductor - hugene10stv1cdf not available >>>>> Error in exprs(rma(VFdata)) : >>>>> ?error in evaluating the argument 'object' in selecting a method for >>>>> function 'exprs' >>>>>> >>>>> >>>>> I'm very inexperienced in terms of stuff like that. A answer for >>>>> dummies would be much appreciated. >>>>> >>>>> Thanks >>>>> >>>>> Christoph >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at stat.math.ethz.ch >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> >>>> >>> >> >
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Thats very complicated and (Sorry) in my case not very useful. My program needs to be able to read a great range of CEL files and schould end up with the same object preferable an AFFYbatch object (or I have to rewrite all my code). I need a standard way to read CEL files were the user is not concerned about the micro-array chip type used to get the CEL files. Is that possible? Thank you very much for your reply though. Christoph On 19 April 2010 12:51, Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> wrote: > btw, if you want to use the affy package, I believe that the package: > > http://www.bioconductor.org/packages/release/data/annotation/html/hu gene10stv1.r3cdf.html > > should suffice (you will need to specify the name of the package to be > used though, check the docs for ReadAffy). > > b > > On Mon, Apr 19, 2010 at 1:48 AM, Benilton Carvalho > <beniltoncarvalho at="" gmail.com=""> wrote: >> Hi Christoph, >> >> the way to do this with oligo is: >> >> library(oligo) >> rawData = read.celfiles(list.celfiles()) >> summaries1 = rma(rawData, target="probeset") >> summaries2 = rma(rawData, target="core") >> >> summaries1 will contain the rma summaries to the probeset defined in >> the PGF file. summaries2 will contain the summaries for the >> metaprobesets defined in the core.mps file. >> >> AffyBatch objects are to be used with the affy package, so that's why >> the pd.hugene package was of no use (b/c pd.hugene is to be used with >> oligo). >> >> hth, >> b >> >> On Mon, Apr 19, 2010 at 1:33 AM, Christoph Knapp >> <mkna005 at="" aucklanduni.ac.nz=""> wrote: >>> I forgot to mention that I tried that as well: >>> >>>> ? ? biocLite("hugene10stv1cdf") >>> Using R version 2.10.1, biocinstall version 2.5.10. >>> Installing Bioconductor version 2.5 packages: >>> [1] "hugene10stv1cdf" >>> Please wait... >>> >>> Warning message: >>> In getDependencies(pkgs, dependencies, available, lib) : >>> ?package ?hugene10stv1cdf? is not available >>> >>> Why is it not possible for me to install that package. >>> >>> Thanks >>> >>> Christoph >>> >>> On 19 April 2010 12:13, Christoph Knapp <mkna005 at="" aucklanduni.ac.nz=""> wrote: >>>> Sorry, >>>> still no change >>>> >>>> AffyBatch object >>>> size of arrays=1050x1050 features (11 kb) >>>> cdf=HuGene-1_0-st-v1 (??? affyids) >>>> number of samples=7 >>>> Error in getCdfInfo(object) : >>>> ?Could not obtain CDF environment, problems encountered: >>>> Specified environment does not contain HuGene-1_0-st-v1 >>>> Library - package hugene10stv1cdf not installed >>>> Bioconductor - hugene10stv1cdf not available >>>> In addition: Warning message: >>>> missing cdf environment! in show(AffyBatch) >>>> >>>> Christoph >>>> >>>> On 19 April 2010 11:51, Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> wrote: >>>>> the pd.hugene package (which I'd expect you to download from BioC) is >>>>> to be used with the oligo package. >>>>> >>>>> b >>>>> >>>>> On Sun, Apr 18, 2010 at 11:51 PM, Christoph Knapp >>>>> <mkna005 at="" aucklanduni.ac.nz=""> wrote: >>>>>> Hi all, >>>>>> I'm trying for quite some time to get an analysis started. I keep >>>>>> getting this Error. >>>>>> >>>>>> Error in getCdfInfo(object) : >>>>>> ?Could not obtain CDF environment, problems encountered: >>>>>> Specified environment does not contain HuGene-1_0-st-v1 >>>>>> Library - package hugene10stv1cdf not installed >>>>>> Bioconductor - hugene10stv1cdf not available >>>>>> Calls: rma ... .local -> indexProbes -> indexProbes -> .local -> getCdfInfo >>>>>> Execution halted >>>>>> >>>>>> I installed all possible packages from there >>>>>> >>>>>> http://www.bioconductor.org/docs/workflows/oligoarrays/ >>>>>> >>>>>> and even downloaded and installed that one >>>>>> >>>>>> http://mbi00206.bio.med.uni- muenchen.de/free/pd.hugene.1.0.st.v1.zip) >>>>>> >>>>>> still no change. >>>>>> >>>>>> What am I missing? >>>>>> >>>>>> It reads in the CEL files >>>>>> >>>>>> VFdata=ReadAffy() >>>>>> >>>>>> but when I look at the VFdata object it already says >>>>>> >>>>>>> VFdata >>>>>> AffyBatch object >>>>>> size of arrays=1050x1050 features (11 kb) >>>>>> cdf=HuGene-1_0-st-v1 (??? affyids) >>>>>> number of samples=7 >>>>>> Error in getCdfInfo(object) : >>>>>> ?Could not obtain CDF environment, problems encountered: >>>>>> Specified environment does not contain HuGene-1_0-st-v1 >>>>>> Library - package hugene10stv1cdf not installed >>>>>> Bioconductor - hugene10stv1cdf not available >>>>>> In addition: Warning message: >>>>>> missing cdf environment! in show(AffyBatch) >>>>>> >>>>>> and going on >>>>>> >>>>>>> eset = exprs(rma(VFdata)) >>>>>> Error in getCdfInfo(object) : >>>>>> ?Could not obtain CDF environment, problems encountered: >>>>>> Specified environment does not contain HuGene-1_0-st-v1 >>>>>> Library - package hugene10stv1cdf not installed >>>>>> Bioconductor - hugene10stv1cdf not available >>>>>> Error in exprs(rma(VFdata)) : >>>>>> ?error in evaluating the argument 'object' in selecting a method for >>>>>> function 'exprs' >>>>>>> >>>>>> >>>>>> I'm very inexperienced in terms of stuff like that. A answer for >>>>>> dummies would be much appreciated. >>>>>> >>>>>> Thanks >>>>>> >>>>>> Christoph >>>>>> >>>>>> _______________________________________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor at stat.math.ethz.ch >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>> >>>>> >>>> >>> >> >
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Hi Christoph, If you need AffyBatch objects, you'll need to stick with the affy package. The affy and oligo packages try to extract the annotation package name from the CEL files and automagically install these packages. But when Affymetrix releases new revisions of the PGF/CDF files, the names of the annotation packages are likely to change (to reflect the revision number). The CEL files, on the other hand, remain the same (this is why you're having "problems"). Sorry if our solution isn't very useful for you, but I hope this clarifies what's going on. Best wishes, benilton On Mon, Apr 19, 2010 at 4:52 AM, Christoph Knapp <mkna005 at="" aucklanduni.ac.nz=""> wrote: > Thats very complicated and (Sorry) in my case not very useful. My > program needs to be able to read a great range of CEL files and > schould end up with the same object preferable an AFFYbatch object (or > I have to rewrite all my code). I need a standard way to read CEL > files were the user is not concerned about the micro-array chip type > used to get the CEL files. Is that possible? > > Thank you very much for your reply though. > > Christoph > > On 19 April 2010 12:51, Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> wrote: >> btw, if you want to use the affy package, I believe that the package: >> >> http://www.bioconductor.org/packages/release/data/annotation/html/h ugene10stv1.r3cdf.html >> >> should suffice (you will need to specify the name of the package to be >> used though, check the docs for ReadAffy). >> >> b >> >> On Mon, Apr 19, 2010 at 1:48 AM, Benilton Carvalho >> <beniltoncarvalho at="" gmail.com=""> wrote: >>> Hi Christoph, >>> >>> the way to do this with oligo is: >>> >>> library(oligo) >>> rawData = read.celfiles(list.celfiles()) >>> summaries1 = rma(rawData, target="probeset") >>> summaries2 = rma(rawData, target="core") >>> >>> summaries1 will contain the rma summaries to the probeset defined in >>> the PGF file. summaries2 will contain the summaries for the >>> metaprobesets defined in the core.mps file. >>> >>> AffyBatch objects are to be used with the affy package, so that's why >>> the pd.hugene package was of no use (b/c pd.hugene is to be used with >>> oligo). >>> >>> hth, >>> b >>> >>> On Mon, Apr 19, 2010 at 1:33 AM, Christoph Knapp >>> <mkna005 at="" aucklanduni.ac.nz=""> wrote: >>>> I forgot to mention that I tried that as well: >>>> >>>>> ? ? biocLite("hugene10stv1cdf") >>>> Using R version 2.10.1, biocinstall version 2.5.10. >>>> Installing Bioconductor version 2.5 packages: >>>> [1] "hugene10stv1cdf" >>>> Please wait... >>>> >>>> Warning message: >>>> In getDependencies(pkgs, dependencies, available, lib) : >>>> ?package ?hugene10stv1cdf? is not available >>>> >>>> Why is it not possible for me to install that package. >>>> >>>> Thanks >>>> >>>> Christoph >>>> >>>> On 19 April 2010 12:13, Christoph Knapp <mkna005 at="" aucklanduni.ac.nz=""> wrote: >>>>> Sorry, >>>>> still no change >>>>> >>>>> AffyBatch object >>>>> size of arrays=1050x1050 features (11 kb) >>>>> cdf=HuGene-1_0-st-v1 (??? affyids) >>>>> number of samples=7 >>>>> Error in getCdfInfo(object) : >>>>> ?Could not obtain CDF environment, problems encountered: >>>>> Specified environment does not contain HuGene-1_0-st-v1 >>>>> Library - package hugene10stv1cdf not installed >>>>> Bioconductor - hugene10stv1cdf not available >>>>> In addition: Warning message: >>>>> missing cdf environment! in show(AffyBatch) >>>>> >>>>> Christoph >>>>> >>>>> On 19 April 2010 11:51, Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> wrote: >>>>>> the pd.hugene package (which I'd expect you to download from BioC) is >>>>>> to be used with the oligo package. >>>>>> >>>>>> b >>>>>> >>>>>> On Sun, Apr 18, 2010 at 11:51 PM, Christoph Knapp >>>>>> <mkna005 at="" aucklanduni.ac.nz=""> wrote: >>>>>>> Hi all, >>>>>>> I'm trying for quite some time to get an analysis started. I keep >>>>>>> getting this Error. >>>>>>> >>>>>>> Error in getCdfInfo(object) : >>>>>>> ?Could not obtain CDF environment, problems encountered: >>>>>>> Specified environment does not contain HuGene-1_0-st-v1 >>>>>>> Library - package hugene10stv1cdf not installed >>>>>>> Bioconductor - hugene10stv1cdf not available >>>>>>> Calls: rma ... .local -> indexProbes -> indexProbes -> .local -> getCdfInfo >>>>>>> Execution halted >>>>>>> >>>>>>> I installed all possible packages from there >>>>>>> >>>>>>> http://www.bioconductor.org/docs/workflows/oligoarrays/ >>>>>>> >>>>>>> and even downloaded and installed that one >>>>>>> >>>>>>> http://mbi00206.bio.med.uni- muenchen.de/free/pd.hugene.1.0.st.v1.zip) >>>>>>> >>>>>>> still no change. >>>>>>> >>>>>>> What am I missing? >>>>>>> >>>>>>> It reads in the CEL files >>>>>>> >>>>>>> VFdata=ReadAffy() >>>>>>> >>>>>>> but when I look at the VFdata object it already says >>>>>>> >>>>>>>> VFdata >>>>>>> AffyBatch object >>>>>>> size of arrays=1050x1050 features (11 kb) >>>>>>> cdf=HuGene-1_0-st-v1 (??? affyids) >>>>>>> number of samples=7 >>>>>>> Error in getCdfInfo(object) : >>>>>>> ?Could not obtain CDF environment, problems encountered: >>>>>>> Specified environment does not contain HuGene-1_0-st-v1 >>>>>>> Library - package hugene10stv1cdf not installed >>>>>>> Bioconductor - hugene10stv1cdf not available >>>>>>> In addition: Warning message: >>>>>>> missing cdf environment! in show(AffyBatch) >>>>>>> >>>>>>> and going on >>>>>>> >>>>>>>> eset = exprs(rma(VFdata)) >>>>>>> Error in getCdfInfo(object) : >>>>>>> ?Could not obtain CDF environment, problems encountered: >>>>>>> Specified environment does not contain HuGene-1_0-st-v1 >>>>>>> Library - package hugene10stv1cdf not installed >>>>>>> Bioconductor - hugene10stv1cdf not available >>>>>>> Error in exprs(rma(VFdata)) : >>>>>>> ?error in evaluating the argument 'object' in selecting a method for >>>>>>> function 'exprs' >>>>>>>> >>>>>>> >>>>>>> I'm very inexperienced in terms of stuff like that. A answer for >>>>>>> dummies would be much appreciated. >>>>>>> >>>>>>> Thanks >>>>>>> >>>>>>> Christoph >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioconductor mailing list >>>>>>> Bioconductor at stat.math.ethz.ch >>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>> >>>>>> >>>>> >>>> >>> >> >
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That works well, thanks a lot, but how I said in a previous email, my project is about writing an application which takes in many different cel files without throwing exceptions. Its about making life easier for people who know even less about that stuff than I do ;-). Thats why I need a way to setup R so that it works without problems in a standard way. Is there a possibility to retrieve information's from the cel files itself what the latest version of annotation package is it needs? Than I could just pass this information into the readAffy() command similar to the way you suggested. Sorry for being a pain and thanks for the help. Christoph On 19 April 2010 23:28, Sherri Christian <sherri at="" mun.ca=""> wrote: > sorry all, I forgot to change the name of the subject > S > > Begin forwarded message: > > From: Sherri Christian <sherri at="" mun.ca=""> > Date: April 19, 2010 8:53:25 AM NDT > To: bioconductor at stat.math.ethz.ch, mkna005 at aucklanduni.ac.nz > Cc: Sherri Christian <sherri at="" mun.ca=""> > Subject: Re: Bioconductor Digest, Vol 86, Issue 19 > Hi Christoph, > First, install the package as suggested by Benilton - the name that you > tried was not correct >>biocLite("hugene10stv1.r3cdf") > Then load the library >>library("hugene10stv1.r3cdf") > Then read in your data >>data <- ReadAffy()? #will read in all CEL files in your working directory > Then tell Affy which cdf file it needs to use- because the name of the CDF > file that Affy thinks it needs is NOT what you downloaded >>data at cdfName <- "hugene10stv1.r3cdf" > Now check your data to be sure that the correct cdf file was used >>data > > good luck, > Sherri > > Date: Mon, 19 Apr 2010 01:51:17 +0100 > From: Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> > To: Christoph Knapp <mkna005 at="" aucklanduni.ac.nz=""> > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Bioconductor - hugene10stv1cdf not available > Message-ID: > <v2se71a39ea1004181751p8be0629cnb483027cda4c1b95 at="" mail.gmail.com=""> > Content-Type: text/plain; charset=windows-1252 > btw, if you want to use the affy package, I believe that the package: > http://www.bioconductor.org/packages/release/data/annotation/html/hu gene10stv1.r3cdf.html > should suffice (you will need to specify the name of the package to be > used though, check the docs for ReadAffy). > b > On Mon, Apr 19, 2010 at 1:48 AM, Benilton Carvalho > <beniltoncarvalho at="" gmail.com=""> wrote: > > Hi Christoph, > the way to do this with oligo is: > library(oligo) > rawData = read.celfiles(list.celfiles()) > summaries1 = rma(rawData, target="probeset") > summaries2 = rma(rawData, target="core") > summaries1 will contain the rma summaries to the probeset defined in > the PGF file. summaries2 will contain the summaries for the > metaprobesets defined in the core.mps file. > AffyBatch objects are to be used with the affy package, so that's why > the pd.hugene package was of no use (b/c pd.hugene is to be used with > oligo). > hth, > b > On Mon, Apr 19, 2010 at 1:33 AM, Christoph Knapp > <mkna005 at="" aucklanduni.ac.nz=""> wrote: > > I forgot to mention that I tried that as well: > > ? ? biocLite("hugene10stv1cdf") > > Using R version 2.10.1, biocinstall version 2.5.10. > Installing Bioconductor version 2.5 packages: > [1] "hugene10stv1cdf" > Please wait... > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > ?package ?hugene10stv1cdf? is not available > Why is it not possible for me to install that package. > Thanks > Christoph > On 19 April 2010 12:13, Christoph Knapp <mkna005 at="" aucklanduni.ac.nz=""> wrote: > > Sorry, > still no change > AffyBatch object > size of arrays=1050x1050 features (11 kb) > cdf=HuGene-1_0-st-v1 (??? affyids) > number of samples=7 > Error in getCdfInfo(object) : > ?Could not obtain CDF environment, problems encountered: > Specified environment does not contain HuGene-1_0-st-v1 > Library - package hugene10stv1cdf not installed > Bioconductor - hugene10stv1cdf not available > In addition: Warning message: > missing cdf environment! in show(AffyBatch) > Christoph > On 19 April 2010 11:51, Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> > wrote: > > the pd.hugene package (which I'd expect you to download from BioC) is > to be used with the oligo package. > b > On Sun, Apr 18, 2010 at 11:51 PM, Christoph Knapp > <mkna005 at="" aucklanduni.ac.nz=""> wrote: > > Hi all, > I'm trying for quite some time to get an analysis started. I keep > getting this Error. > Error in getCdfInfo(object) : > ?Could not obtain CDF environment, problems encountered: > Specified environment does not contain HuGene-1_0-st-v1 > Library - package hugene10stv1cdf not installed > Bioconductor - hugene10stv1cdf not available > Calls: rma ... .local -> indexProbes -> indexProbes -> .local -> getCdfInfo > Execution halted > I installed all possible packages from there > http://www.bioconductor.org/docs/workflows/oligoarrays/ > and even downloaded and installed that one > http://mbi00206.bio.med.uni- muenchen.de/free/pd.hugene.1.0.st.v1.zip) > still no change. > What am I missing? > It reads in the CEL files > VFdata=ReadAffy() > but when I look at the VFdata object it already says > > VFdata > > AffyBatch object > size of arrays=1050x1050 features (11 kb) > cdf=HuGene-1_0-st-v1 (??? affyids) > number of samples=7 > Error in getCdfInfo(object) : > ?Could not obtain CDF environment, problems encountered: > Specified environment does not contain HuGene-1_0-st-v1 > Library - package hugene10stv1cdf not installed > Bioconductor - hugene10stv1cdf not available > In addition: Warning message: > missing cdf environment! in show(AffyBatch) > and going on > > eset = exprs(rma(VFdata)) > > Error in getCdfInfo(object) : > ?Could not obtain CDF environment, problems encountered: > Specified environment does not contain HuGene-1_0-st-v1 > Library - package hugene10stv1cdf not installed > Bioconductor - hugene10stv1cdf not available > Error in exprs(rma(VFdata)) : > ?error in evaluating the argument 'object' in selecting a method for > function 'exprs' > > > > I'm very inexperienced in terms of stuff like that. A answer for > dummies would be much appreciated. > Thanks > Christoph > >
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Christoph, I do not have a lot of experience with Bioconductor but my experience is that for some chips (ie. mouse4302), the information is retrieved automatically but for the hugene10 chip it is not. My understanding is that it is because of the syntax of the file that is suggested by the CEL file (this is what I understood from the vignettes). If you want to set up for other people then the best way is probably to set up text files (or TinnR files) that have all the essential "start-up" commands on a "per chip" basis. This is pretty much the limit of my knowledge! Sherri On 19-Apr-10, at 7:30 PM, Christoph Knapp wrote: > That works well, thanks a lot, but how I said in a previous email, my > project is about writing an application which takes in many different > cel files without throwing exceptions. Its about making life easier > for people who know even less about that stuff than I do ;-). Thats > why I need a way to setup R so that it works without problems in a > standard way. Is there a possibility to retrieve information's from > the cel files itself what the latest version of annotation package is > it needs? Than I could just pass this information into the readAffy() > command similar to the way you suggested. > > Sorry for being a pain and thanks for the help. > > Christoph > > On 19 April 2010 23:28, Sherri Christian <sherri at="" mun.ca=""> wrote: >> sorry all, I forgot to change the name of the subject >> S >> >> Begin forwarded message: >> >> From: Sherri Christian <sherri at="" mun.ca=""> >> Date: April 19, 2010 8:53:25 AM NDT >> To: bioconductor at stat.math.ethz.ch, mkna005 at aucklanduni.ac.nz >> Cc: Sherri Christian <sherri at="" mun.ca=""> >> Subject: Re: Bioconductor Digest, Vol 86, Issue 19 >> Hi Christoph, >> First, install the package as suggested by Benilton - the name >> that you >> tried was not correct >>> biocLite("hugene10stv1.r3cdf") >> Then load the library >>> library("hugene10stv1.r3cdf") >> Then read in your data >>> data <- ReadAffy() #will read in all CEL files in your working >>> directory >> Then tell Affy which cdf file it needs to use- because the name of >> the CDF >> file that Affy thinks it needs is NOT what you downloaded >>> data at cdfName <- "hugene10stv1.r3cdf" >> Now check your data to be sure that the correct cdf file was used >>> data >> >> good luck, >> Sherri >> >> Date: Mon, 19 Apr 2010 01:51:17 +0100 >> From: Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> >> To: Christoph Knapp <mkna005 at="" aucklanduni.ac.nz=""> >> Cc: bioconductor at stat.math.ethz.ch >> Subject: Re: [BioC] Bioconductor - hugene10stv1cdf not available >> Message-ID: >> <v2se71a39ea1004181751p8be0629cnb483027cda4c1b95 at="" mail.gmail.com=""> >> Content-Type: text/plain; charset=windows-1252 >> btw, if you want to use the affy package, I believe that the package: >> http://www.bioconductor.org/packages/release/data/annotation/html/ >> hugene10stv1.r3cdf.html >> should suffice (you will need to specify the name of the package >> to be >> used though, check the docs for ReadAffy). >> b >> On Mon, Apr 19, 2010 at 1:48 AM, Benilton Carvalho >> <beniltoncarvalho at="" gmail.com=""> wrote: >> >> Hi Christoph, >> the way to do this with oligo is: >> library(oligo) >> rawData = read.celfiles(list.celfiles()) >> summaries1 = rma(rawData, target="probeset") >> summaries2 = rma(rawData, target="core") >> summaries1 will contain the rma summaries to the probeset defined in >> the PGF file. summaries2 will contain the summaries for the >> metaprobesets defined in the core.mps file. >> AffyBatch objects are to be used with the affy package, so that's why >> the pd.hugene package was of no use (b/c pd.hugene is to be used with >> oligo). >> hth, >> b >> On Mon, Apr 19, 2010 at 1:33 AM, Christoph Knapp >> <mkna005 at="" aucklanduni.ac.nz=""> wrote: >> >> I forgot to mention that I tried that as well: >> >> ? ? biocLite("hugene10stv1cdf") >> >> Using R version 2.10.1, biocinstall version 2.5.10. >> Installing Bioconductor version 2.5 packages: >> [1] "hugene10stv1cdf" >> Please wait... >> Warning message: >> In getDependencies(pkgs, dependencies, available, lib) : >> ?package ?hugene10stv1cdf? is not available >> Why is it not possible for me to install that package. >> Thanks >> Christoph >> On 19 April 2010 12:13, Christoph Knapp >> <mkna005 at="" aucklanduni.ac.nz=""> wrote: >> >> Sorry, >> still no change >> AffyBatch object >> size of arrays=1050x1050 features (11 kb) >> cdf=HuGene-1_0-st-v1 (??? affyids) >> number of samples=7 >> Error in getCdfInfo(object) : >> ?Could not obtain CDF environment, problems encountered: >> Specified environment does not contain HuGene-1_0-st-v1 >> Library - package hugene10stv1cdf not installed >> Bioconductor - hugene10stv1cdf not available >> In addition: Warning message: >> missing cdf environment! in show(AffyBatch) >> Christoph >> On 19 April 2010 11:51, Benilton Carvalho >> <beniltoncarvalho at="" gmail.com=""> >> wrote: >> >> the pd.hugene package (which I'd expect you to download from BioC) is >> to be used with the oligo package. >> b >> On Sun, Apr 18, 2010 at 11:51 PM, Christoph Knapp >> <mkna005 at="" aucklanduni.ac.nz=""> wrote: >> >> Hi all, >> I'm trying for quite some time to get an analysis started. I keep >> getting this Error. >> Error in getCdfInfo(object) : >> ?Could not obtain CDF environment, problems encountered: >> Specified environment does not contain HuGene-1_0-st-v1 >> Library - package hugene10stv1cdf not installed >> Bioconductor - hugene10stv1cdf not available >> Calls: rma ... .local -> indexProbes -> indexProbes -> .local -> >> getCdfInfo >> Execution halted >> I installed all possible packages from there >> http://www.bioconductor.org/docs/workflows/oligoarrays/ >> and even downloaded and installed that one >> http://mbi00206.bio.med.uni- muenchen.de/free/pd.hugene.1.0.st.v1.zip) >> still no change. >> What am I missing? >> It reads in the CEL files >> VFdata=ReadAffy() >> but when I look at the VFdata object it already says >> >> VFdata >> >> AffyBatch object >> size of arrays=1050x1050 features (11 kb) >> cdf=HuGene-1_0-st-v1 (??? affyids) >> number of samples=7 >> Error in getCdfInfo(object) : >> ?Could not obtain CDF environment, problems encountered: >> Specified environment does not contain HuGene-1_0-st-v1 >> Library - package hugene10stv1cdf not installed >> Bioconductor - hugene10stv1cdf not available >> In addition: Warning message: >> missing cdf environment! in show(AffyBatch) >> and going on >> >> eset = exprs(rma(VFdata)) >> >> Error in getCdfInfo(object) : >> ?Could not obtain CDF environment, problems encountered: >> Specified environment does not contain HuGene-1_0-st-v1 >> Library - package hugene10stv1cdf not installed >> Bioconductor - hugene10stv1cdf not available >> Error in exprs(rma(VFdata)) : >> ?error in evaluating the argument 'object' in selecting a method for >> function 'exprs' >> >> >> >> I'm very inexperienced in terms of stuff like that. A answer for >> dummies would be much appreciated. >> Thanks >> Christoph >> >>
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Now I'm getting following error. This chip type gives me a headache and if I go on probably gastric ulcer to. Error in setQCEnvironment(cdfn) : Could not find array definition file ' hugene10stv1.r3cdf.qcdef '. Simpleaffy does not know the QC parameters for this array type. See the package vignette for details about how to specify QC parameters manually. Calls: qc -> qc -> qc.affy -> setQCEnvironment Execution halted This happens in QCReport(VFdata,file=paste(totalJobpath,"\\","AffyQCReport.pdf",sep="" )) It generates some of the report but not all. I tried setQCEnvironment(cleancdfname(cdfName(eset))) as suggested in http://127.0.0.1:25446/library/simpleaffy/html/setQCEnvironment.html but that did not help. Please help? Christoph On 20 April 2010 11:03, Sherri Christian <sherri at="" mun.ca=""> wrote: > Christoph, > > I do not have a lot of experience with Bioconductor but my experience is > that for some chips (ie. mouse4302), the information is retrieved > automatically but for the hugene10 chip it is not. My understanding is that > it is because of the syntax of the file that is suggested by the CEL file > (this is what I understood from the vignettes). If you want to set up for > other people then the best way is probably to set up text files (or TinnR > files) that have all the essential "start-up" commands on a "per chip" > basis. This is pretty much the limit of my knowledge! > > Sherri > > On 19-Apr-10, at 7:30 PM, Christoph Knapp wrote: > >> That works well, thanks a lot, but how I said in a previous email, my >> project is about writing an application which takes in many different >> cel files without throwing exceptions. Its about making life easier >> for people who know even less about that stuff than I do ;-). Thats >> why I need a way to setup R so that it works without problems in a >> standard way. Is there a possibility to retrieve information's from >> the cel files itself what the latest version of annotation package is >> it needs? Than I could just pass this information into the readAffy() >> command similar to the way you suggested. >> >> Sorry for being a pain and thanks for the help. >> >> Christoph >> >> On 19 April 2010 23:28, Sherri Christian <sherri at="" mun.ca=""> wrote: >>> >>> sorry all, I forgot to change the name of the subject >>> S >>> >>> Begin forwarded message: >>> >>> From: Sherri Christian <sherri at="" mun.ca=""> >>> Date: April 19, 2010 8:53:25 AM NDT >>> To: bioconductor at stat.math.ethz.ch, mkna005 at aucklanduni.ac.nz >>> Cc: Sherri Christian <sherri at="" mun.ca=""> >>> Subject: Re: Bioconductor Digest, Vol 86, Issue 19 >>> Hi Christoph, >>> First, install the package as suggested by Benilton - the name that you >>> tried was not correct >>>> >>>> biocLite("hugene10stv1.r3cdf") >>> >>> Then load the library >>>> >>>> library("hugene10stv1.r3cdf") >>> >>> Then read in your data >>>> >>>> data <- ReadAffy() ?#will read in all CEL files in your working >>>> directory >>> >>> Then tell Affy which cdf file it needs to use- because the name of the >>> CDF >>> file that Affy thinks it needs is NOT what you downloaded >>>> >>>> data at cdfName <- "hugene10stv1.r3cdf" >>> >>> Now check your data to be sure that the correct cdf file was used >>>> >>>> data >>> >>> good luck, >>> Sherri >>> >>> Date: Mon, 19 Apr 2010 01:51:17 +0100 >>> From: Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> >>> To: Christoph Knapp <mkna005 at="" aucklanduni.ac.nz=""> >>> Cc: bioconductor at stat.math.ethz.ch >>> Subject: Re: [BioC] Bioconductor - hugene10stv1cdf not available >>> Message-ID: >>> <v2se71a39ea1004181751p8be0629cnb483027cda4c1b95 at="" mail.gmail.com=""> >>> Content-Type: text/plain; charset=windows-1252 >>> btw, if you want to use the affy package, I believe that the package: >>> >>> http://www.bioconductor.org/packages/release/data/annotation/html/ hugene10stv1.r3cdf.html >>> should suffice (you will need to specify the name of the package to be >>> used though, check the docs for ReadAffy). >>> b >>> On Mon, Apr 19, 2010 at 1:48 AM, Benilton Carvalho >>> <beniltoncarvalho at="" gmail.com=""> wrote: >>> >>> Hi Christoph, >>> the way to do this with oligo is: >>> library(oligo) >>> rawData = read.celfiles(list.celfiles()) >>> summaries1 = rma(rawData, target="probeset") >>> summaries2 = rma(rawData, target="core") >>> summaries1 will contain the rma summaries to the probeset defined in >>> the PGF file. summaries2 will contain the summaries for the >>> metaprobesets defined in the core.mps file. >>> AffyBatch objects are to be used with the affy package, so that's why >>> the pd.hugene package was of no use (b/c pd.hugene is to be used with >>> oligo). >>> hth, >>> b >>> On Mon, Apr 19, 2010 at 1:33 AM, Christoph Knapp >>> <mkna005 at="" aucklanduni.ac.nz=""> wrote: >>> >>> I forgot to mention that I tried that as well: >>> >>> ? ? biocLite("hugene10stv1cdf") >>> >>> Using R version 2.10.1, biocinstall version 2.5.10. >>> Installing Bioconductor version 2.5 packages: >>> [1] "hugene10stv1cdf" >>> Please wait... >>> Warning message: >>> In getDependencies(pkgs, dependencies, available, lib) : >>> ?package ?hugene10stv1cdf? is not available >>> Why is it not possible for me to install that package. >>> Thanks >>> Christoph >>> On 19 April 2010 12:13, Christoph Knapp <mkna005 at="" aucklanduni.ac.nz=""> >>> wrote: >>> >>> Sorry, >>> still no change >>> AffyBatch object >>> size of arrays=1050x1050 features (11 kb) >>> cdf=HuGene-1_0-st-v1 (??? affyids) >>> number of samples=7 >>> Error in getCdfInfo(object) : >>> ?Could not obtain CDF environment, problems encountered: >>> Specified environment does not contain HuGene-1_0-st-v1 >>> Library - package hugene10stv1cdf not installed >>> Bioconductor - hugene10stv1cdf not available >>> In addition: Warning message: >>> missing cdf environment! in show(AffyBatch) >>> Christoph >>> On 19 April 2010 11:51, Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> >>> wrote: >>> >>> the pd.hugene package (which I'd expect you to download from BioC) is >>> to be used with the oligo package. >>> b >>> On Sun, Apr 18, 2010 at 11:51 PM, Christoph Knapp >>> <mkna005 at="" aucklanduni.ac.nz=""> wrote: >>> >>> Hi all, >>> I'm trying for quite some time to get an analysis started. I keep >>> getting this Error. >>> Error in getCdfInfo(object) : >>> ?Could not obtain CDF environment, problems encountered: >>> Specified environment does not contain HuGene-1_0-st-v1 >>> Library - package hugene10stv1cdf not installed >>> Bioconductor - hugene10stv1cdf not available >>> Calls: rma ... .local -> indexProbes -> indexProbes -> .local -> >>> getCdfInfo >>> Execution halted >>> I installed all possible packages from there >>> http://www.bioconductor.org/docs/workflows/oligoarrays/ >>> and even downloaded and installed that one >>> http://mbi00206.bio.med.uni- muenchen.de/free/pd.hugene.1.0.st.v1.zip) >>> still no change. >>> What am I missing? >>> It reads in the CEL files >>> VFdata=ReadAffy() >>> but when I look at the VFdata object it already says >>> >>> VFdata >>> >>> AffyBatch object >>> size of arrays=1050x1050 features (11 kb) >>> cdf=HuGene-1_0-st-v1 (??? affyids) >>> number of samples=7 >>> Error in getCdfInfo(object) : >>> ?Could not obtain CDF environment, problems encountered: >>> Specified environment does not contain HuGene-1_0-st-v1 >>> Library - package hugene10stv1cdf not installed >>> Bioconductor - hugene10stv1cdf not available >>> In addition: Warning message: >>> missing cdf environment! in show(AffyBatch) >>> and going on >>> >>> eset = exprs(rma(VFdata)) >>> >>> Error in getCdfInfo(object) : >>> ?Could not obtain CDF environment, problems encountered: >>> Specified environment does not contain HuGene-1_0-st-v1 >>> Library - package hugene10stv1cdf not installed >>> Bioconductor - hugene10stv1cdf not available >>> Error in exprs(rma(VFdata)) : >>> ?error in evaluating the argument 'object' in selecting a method for >>> function 'exprs' >>> >>> >>> >>> I'm very inexperienced in terms of stuff like that. A answer for >>> dummies would be much appreciated. >>> Thanks >>> Christoph >>> >>> > >
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On Mon, Apr 19, 2010 at 8:25 PM, Christoph Knapp <mkna005@aucklanduni.ac.nz>wrote: > Now I'm getting following error. This chip type gives me a headache > and if I go on probably gastric ulcer to. > > Error in setQCEnvironment(cdfn) : > Could not find array definition file ' hugene10stv1.r3cdf.qcdef '. > Simpleaffy does not know the QC parameters for this array type. > See the package vignette for details about how to specify QC > parameters manually. > Calls: qc -> qc -> qc.affy -> setQCEnvironment > Execution halted > > This happens in > > QCReport(VFdata,file=paste(totalJobpath,"\\","AffyQCReport.pdf",sep= "")) > > It generates some of the report but not all. > > I tried > > setQCEnvironment(cleancdfname(cdfName(eset))) > > as suggested in > > http://127.0.0.1:25446/library/simpleaffy/html/setQCEnvironment.html > > but that did not help. > > Please help? > > Hi, Christoph. You will definitely want to get in the habit of reading and following the posting guide before posting. I think I answered this question a couple of days ago for another person. In any case, did you follow the hint in the error message? If you did and are still having problems, be sure to post the code, the error, and sessionInfo(). Hope that helps. Sean > Christoph > > On 20 April 2010 11:03, Sherri Christian <sherri@mun.ca> wrote: > > Christoph, > > > > I do not have a lot of experience with Bioconductor but my experience is > > that for some chips (ie. mouse4302), the information is retrieved > > automatically but for the hugene10 chip it is not. My understanding is > that > > it is because of the syntax of the file that is suggested by the CEL file > > (this is what I understood from the vignettes). If you want to set up for > > other people then the best way is probably to set up text files (or TinnR > > files) that have all the essential "start-up" commands on a "per chip" > > basis. This is pretty much the limit of my knowledge! > > > > Sherri > > > > On 19-Apr-10, at 7:30 PM, Christoph Knapp wrote: > > > >> That works well, thanks a lot, but how I said in a previous email, my > >> project is about writing an application which takes in many different > >> cel files without throwing exceptions. Its about making life easier > >> for people who know even less about that stuff than I do ;-). Thats > >> why I need a way to setup R so that it works without problems in a > >> standard way. Is there a possibility to retrieve information's from > >> the cel files itself what the latest version of annotation package is > >> it needs? Than I could just pass this information into the readAffy() > >> command similar to the way you suggested. > >> > >> Sorry for being a pain and thanks for the help. > >> > >> Christoph > >> > >> On 19 April 2010 23:28, Sherri Christian <sherri@mun.ca> wrote: > >>> > >>> sorry all, I forgot to change the name of the subject > >>> S > >>> > >>> Begin forwarded message: > >>> > >>> From: Sherri Christian <sherri@mun.ca> > >>> Date: April 19, 2010 8:53:25 AM NDT > >>> To: bioconductor@stat.math.ethz.ch, mkna005@aucklanduni.ac.nz > >>> Cc: Sherri Christian <sherri@mun.ca> > >>> Subject: Re: Bioconductor Digest, Vol 86, Issue 19 > >>> Hi Christoph, > >>> First, install the package as suggested by Benilton - the name that you > >>> tried was not correct > >>>> > >>>> biocLite("hugene10stv1.r3cdf") > >>> > >>> Then load the library > >>>> > >>>> library("hugene10stv1.r3cdf") > >>> > >>> Then read in your data > >>>> > >>>> data <- ReadAffy() #will read in all CEL files in your working > >>>> directory > >>> > >>> Then tell Affy which cdf file it needs to use- because the name of the > >>> CDF > >>> file that Affy thinks it needs is NOT what you downloaded > >>>> > >>>> data@cdfName <- "hugene10stv1.r3cdf" > >>> > >>> Now check your data to be sure that the correct cdf file was used > >>>> > >>>> data > >>> > >>> good luck, > >>> Sherri > >>> > >>> Date: Mon, 19 Apr 2010 01:51:17 +0100 > >>> From: Benilton Carvalho <beniltoncarvalho@gmail.com> > >>> To: Christoph Knapp <mkna005@aucklanduni.ac.nz> > >>> Cc: bioconductor@stat.math.ethz.ch > >>> Subject: Re: [BioC] Bioconductor - hugene10stv1cdf not available > >>> Message-ID: > >>> <v2se71a39ea1004181751p8be0629cnb483027cda4c1b95@mail.gmail.com> > >>> Content-Type: text/plain; charset=windows-1252 > >>> btw, if you want to use the affy package, I believe that the package: > >>> > >>> > http://www.bioconductor.org/packages/release/data/annotation/html/hu gene10stv1.r3cdf.html > >>> should suffice (you will need to specify the name of the package to be > >>> used though, check the docs for ReadAffy). > >>> b > >>> On Mon, Apr 19, 2010 at 1:48 AM, Benilton Carvalho > >>> <beniltoncarvalho@gmail.com> wrote: > >>> > >>> Hi Christoph, > >>> the way to do this with oligo is: > >>> library(oligo) > >>> rawData = read.celfiles(list.celfiles()) > >>> summaries1 = rma(rawData, target="probeset") > >>> summaries2 = rma(rawData, target="core") > >>> summaries1 will contain the rma summaries to the probeset defined in > >>> the PGF file. summaries2 will contain the summaries for the > >>> metaprobesets defined in the core.mps file. > >>> AffyBatch objects are to be used with the affy package, so that's why > >>> the pd.hugene package was of no use (b/c pd.hugene is to be used with > >>> oligo). > >>> hth, > >>> b > >>> On Mon, Apr 19, 2010 at 1:33 AM, Christoph Knapp > >>> <mkna005@aucklanduni.ac.nz> wrote: > >>> > >>> I forgot to mention that I tried that as well: > >>> > >>> ? ? biocLite("hugene10stv1cdf") > >>> > >>> Using R version 2.10.1, biocinstall version 2.5.10. > >>> Installing Bioconductor version 2.5 packages: > >>> [1] "hugene10stv1cdf" > >>> Please wait... > >>> Warning message: > >>> In getDependencies(pkgs, dependencies, available, lib) : > >>> ?package ?hugene10stv1cdf? is not available > >>> Why is it not possible for me to install that package. > >>> Thanks > >>> Christoph > >>> On 19 April 2010 12:13, Christoph Knapp <mkna005@aucklanduni.ac.nz> > >>> wrote: > >>> > >>> Sorry, > >>> still no change > >>> AffyBatch object > >>> size of arrays=1050x1050 features (11 kb) > >>> cdf=HuGene-1_0-st-v1 (??? affyids) > >>> number of samples=7 > >>> Error in getCdfInfo(object) : > >>> ?Could not obtain CDF environment, problems encountered: > >>> Specified environment does not contain HuGene-1_0-st-v1 > >>> Library - package hugene10stv1cdf not installed > >>> Bioconductor - hugene10stv1cdf not available > >>> In addition: Warning message: > >>> missing cdf environment! in show(AffyBatch) > >>> Christoph > >>> On 19 April 2010 11:51, Benilton Carvalho <beniltoncarvalho@gmail.com> > >>> wrote: > >>> > >>> the pd.hugene package (which I'd expect you to download from BioC) is > >>> to be used with the oligo package. > >>> b > >>> On Sun, Apr 18, 2010 at 11:51 PM, Christoph Knapp > >>> <mkna005@aucklanduni.ac.nz> wrote: > >>> > >>> Hi all, > >>> I'm trying for quite some time to get an analysis started. I keep > >>> getting this Error. > >>> Error in getCdfInfo(object) : > >>> ?Could not obtain CDF environment, problems encountered: > >>> Specified environment does not contain HuGene-1_0-st-v1 > >>> Library - package hugene10stv1cdf not installed > >>> Bioconductor - hugene10stv1cdf not available > >>> Calls: rma ... .local -> indexProbes -> indexProbes -> .local -> > >>> getCdfInfo > >>> Execution halted > >>> I installed all possible packages from there > >>> http://www.bioconductor.org/docs/workflows/oligoarrays/ > >>> and even downloaded and installed that one > >>> http://mbi00206.bio.med.uni- muenchen.de/free/pd.hugene.1.0.st.v1.zip) > >>> still no change. > >>> What am I missing? > >>> It reads in the CEL files > >>> VFdata=ReadAffy() > >>> but when I look at the VFdata object it already says > >>> > >>> VFdata > >>> > >>> AffyBatch object > >>> size of arrays=1050x1050 features (11 kb) > >>> cdf=HuGene-1_0-st-v1 (??? affyids) > >>> number of samples=7 > >>> Error in getCdfInfo(object) : > >>> ?Could not obtain CDF environment, problems encountered: > >>> Specified environment does not contain HuGene-1_0-st-v1 > >>> Library - package hugene10stv1cdf not installed > >>> Bioconductor - hugene10stv1cdf not available > >>> In addition: Warning message: > >>> missing cdf environment! in show(AffyBatch) > >>> and going on > >>> > >>> eset = exprs(rma(VFdata)) > >>> > >>> Error in getCdfInfo(object) : > >>> ?Could not obtain CDF environment, problems encountered: > >>> Specified environment does not contain HuGene-1_0-st-v1 > >>> Library - package hugene10stv1cdf not installed > >>> Bioconductor - hugene10stv1cdf not available > >>> Error in exprs(rma(VFdata)) : > >>> ?error in evaluating the argument 'object' in selecting a method for > >>> function 'exprs' > >>> > >>> > >>> > >>> I'm very inexperienced in terms of stuff like that. A answer for > >>> dummies would be much appreciated. > >>> Thanks > >>> Christoph > >>> > >>> > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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Christoph Knapp wrote: > Now I'm getting following error. This chip type gives me a headache > and if I go on probably gastric ulcer to. This is (again) something that has been asked and answered many times on this list. And it is a case study in what happens when one uses tools blindly without knowing what the tool is designed for. A quick peek at the vignettes makes me think that this isn't explicitly spelled out, which is definitely a problem. However, before embarking on the analysis of some data, it is IMO very important to know at least a little bit about the underlying analysis methodology and what data you are working with (and that's on you). The simpleaffy package is designed for the so-called 3'-biased arrays, which used a T7-oligo(dT) primer that binds to the poly-A tail of mRNA, in order to do the in vitro translation. Because of this, the resulting cDNA tends to be 3' biased, so it is a good idea to see how bad the bias is, which indicates how well (or poorly) the IVT step worked. In addition, the 3'-biased arrays (almost) all have both PM and MM probes, which are both required for some of the quality control steps in the simpleaffy package. The HuGene array does not use the T7-Oligo(dT) primer, instead, the IVT step uses random primers, so the concern over 3'-bias is negligible. In addition, the HuGene array is PM-only, so any quality control step that uses MAS5 or computes present/absent calls is not going to work. Because of this, it doesn't make much sense to use the simpleaffy package to do quality control of the HuGene chip. Best, Jim > > Error in setQCEnvironment(cdfn) : > Could not find array definition file ' hugene10stv1.r3cdf.qcdef '. > Simpleaffy does not know the QC parameters for this array type. > See the package vignette for details about how to specify QC > parameters manually. > Calls: qc -> qc -> qc.affy -> setQCEnvironment > Execution halted > > This happens in > > QCReport(VFdata,file=paste(totalJobpath,"\\","AffyQCReport.pdf",sep= "")) > > It generates some of the report but not all. > > I tried > > setQCEnvironment(cleancdfname(cdfName(eset))) > > as suggested in > > http://127.0.0.1:25446/library/simpleaffy/html/setQCEnvironment.html > > but that did not help. > > Please help? > > Christoph > > On 20 April 2010 11:03, Sherri Christian <sherri at="" mun.ca=""> wrote: >> Christoph, >> >> I do not have a lot of experience with Bioconductor but my experience is >> that for some chips (ie. mouse4302), the information is retrieved >> automatically but for the hugene10 chip it is not. My understanding is that >> it is because of the syntax of the file that is suggested by the CEL file >> (this is what I understood from the vignettes). If you want to set up for >> other people then the best way is probably to set up text files (or TinnR >> files) that have all the essential "start-up" commands on a "per chip" >> basis. This is pretty much the limit of my knowledge! >> >> Sherri >> >> On 19-Apr-10, at 7:30 PM, Christoph Knapp wrote: >> >>> That works well, thanks a lot, but how I said in a previous email, my >>> project is about writing an application which takes in many different >>> cel files without throwing exceptions. Its about making life easier >>> for people who know even less about that stuff than I do ;-). Thats >>> why I need a way to setup R so that it works without problems in a >>> standard way. Is there a possibility to retrieve information's from >>> the cel files itself what the latest version of annotation package is >>> it needs? Than I could just pass this information into the readAffy() >>> command similar to the way you suggested. >>> >>> Sorry for being a pain and thanks for the help. >>> >>> Christoph >>> >>> On 19 April 2010 23:28, Sherri Christian <sherri at="" mun.ca=""> wrote: >>>> sorry all, I forgot to change the name of the subject >>>> S >>>> >>>> Begin forwarded message: >>>> >>>> From: Sherri Christian <sherri at="" mun.ca=""> >>>> Date: April 19, 2010 8:53:25 AM NDT >>>> To: bioconductor at stat.math.ethz.ch, mkna005 at aucklanduni.ac.nz >>>> Cc: Sherri Christian <sherri at="" mun.ca=""> >>>> Subject: Re: Bioconductor Digest, Vol 86, Issue 19 >>>> Hi Christoph, >>>> First, install the package as suggested by Benilton - the name that you >>>> tried was not correct >>>>> biocLite("hugene10stv1.r3cdf") >>>> Then load the library >>>>> library("hugene10stv1.r3cdf") >>>> Then read in your data >>>>> data <- ReadAffy() #will read in all CEL files in your working >>>>> directory >>>> Then tell Affy which cdf file it needs to use- because the name of the >>>> CDF >>>> file that Affy thinks it needs is NOT what you downloaded >>>>> data at cdfName <- "hugene10stv1.r3cdf" >>>> Now check your data to be sure that the correct cdf file was used >>>>> data >>>> good luck, >>>> Sherri >>>> >>>> Date: Mon, 19 Apr 2010 01:51:17 +0100 >>>> From: Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> >>>> To: Christoph Knapp <mkna005 at="" aucklanduni.ac.nz=""> >>>> Cc: bioconductor at stat.math.ethz.ch >>>> Subject: Re: [BioC] Bioconductor - hugene10stv1cdf not available >>>> Message-ID: >>>> <v2se71a39ea1004181751p8be0629cnb483027cda4c1b95 at="" mail.gmail.com=""> >>>> Content-Type: text/plain; charset=windows-1252 >>>> btw, if you want to use the affy package, I believe that the package: >>>> >>>> http://www.bioconductor.org/packages/release/data/annotation/html /hugene10stv1.r3cdf.html >>>> should suffice (you will need to specify the name of the package to be >>>> used though, check the docs for ReadAffy). >>>> b >>>> On Mon, Apr 19, 2010 at 1:48 AM, Benilton Carvalho >>>> <beniltoncarvalho at="" gmail.com=""> wrote: >>>> >>>> Hi Christoph, >>>> the way to do this with oligo is: >>>> library(oligo) >>>> rawData = read.celfiles(list.celfiles()) >>>> summaries1 = rma(rawData, target="probeset") >>>> summaries2 = rma(rawData, target="core") >>>> summaries1 will contain the rma summaries to the probeset defined in >>>> the PGF file. summaries2 will contain the summaries for the >>>> metaprobesets defined in the core.mps file. >>>> AffyBatch objects are to be used with the affy package, so that's why >>>> the pd.hugene package was of no use (b/c pd.hugene is to be used with >>>> oligo). >>>> hth, >>>> b >>>> On Mon, Apr 19, 2010 at 1:33 AM, Christoph Knapp >>>> <mkna005 at="" aucklanduni.ac.nz=""> wrote: >>>> >>>> I forgot to mention that I tried that as well: >>>> >>>> ? ? biocLite("hugene10stv1cdf") >>>> >>>> Using R version 2.10.1, biocinstall version 2.5.10. >>>> Installing Bioconductor version 2.5 packages: >>>> [1] "hugene10stv1cdf" >>>> Please wait... >>>> Warning message: >>>> In getDependencies(pkgs, dependencies, available, lib) : >>>> ?package ?hugene10stv1cdf? is not available >>>> Why is it not possible for me to install that package. >>>> Thanks >>>> Christoph >>>> On 19 April 2010 12:13, Christoph Knapp <mkna005 at="" aucklanduni.ac.nz=""> >>>> wrote: >>>> >>>> Sorry, >>>> still no change >>>> AffyBatch object >>>> size of arrays=1050x1050 features (11 kb) >>>> cdf=HuGene-1_0-st-v1 (??? affyids) >>>> number of samples=7 >>>> Error in getCdfInfo(object) : >>>> ?Could not obtain CDF environment, problems encountered: >>>> Specified environment does not contain HuGene-1_0-st-v1 >>>> Library - package hugene10stv1cdf not installed >>>> Bioconductor - hugene10stv1cdf not available >>>> In addition: Warning message: >>>> missing cdf environment! in show(AffyBatch) >>>> Christoph >>>> On 19 April 2010 11:51, Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> >>>> wrote: >>>> >>>> the pd.hugene package (which I'd expect you to download from BioC) is >>>> to be used with the oligo package. >>>> b >>>> On Sun, Apr 18, 2010 at 11:51 PM, Christoph Knapp >>>> <mkna005 at="" aucklanduni.ac.nz=""> wrote: >>>> >>>> Hi all, >>>> I'm trying for quite some time to get an analysis started. I keep >>>> getting this Error. >>>> Error in getCdfInfo(object) : >>>> ?Could not obtain CDF environment, problems encountered: >>>> Specified environment does not contain HuGene-1_0-st-v1 >>>> Library - package hugene10stv1cdf not installed >>>> Bioconductor - hugene10stv1cdf not available >>>> Calls: rma ... .local -> indexProbes -> indexProbes -> .local -> >>>> getCdfInfo >>>> Execution halted >>>> I installed all possible packages from there >>>> http://www.bioconductor.org/docs/workflows/oligoarrays/ >>>> and even downloaded and installed that one >>>> http://mbi00206.bio.med.uni- muenchen.de/free/pd.hugene.1.0.st.v1.zip) >>>> still no change. >>>> What am I missing? >>>> It reads in the CEL files >>>> VFdata=ReadAffy() >>>> but when I look at the VFdata object it already says >>>> >>>> VFdata >>>> >>>> AffyBatch object >>>> size of arrays=1050x1050 features (11 kb) >>>> cdf=HuGene-1_0-st-v1 (??? affyids) >>>> number of samples=7 >>>> Error in getCdfInfo(object) : >>>> ?Could not obtain CDF environment, problems encountered: >>>> Specified environment does not contain HuGene-1_0-st-v1 >>>> Library - package hugene10stv1cdf not installed >>>> Bioconductor - hugene10stv1cdf not available >>>> In addition: Warning message: >>>> missing cdf environment! in show(AffyBatch) >>>> and going on >>>> >>>> eset = exprs(rma(VFdata)) >>>> >>>> Error in getCdfInfo(object) : >>>> ?Could not obtain CDF environment, problems encountered: >>>> Specified environment does not contain HuGene-1_0-st-v1 >>>> Library - package hugene10stv1cdf not installed >>>> Bioconductor - hugene10stv1cdf not available >>>> Error in exprs(rma(VFdata)) : >>>> ?error in evaluating the argument 'object' in selecting a method for >>>> function 'exprs' >>>> >>>> >>>> >>>> I'm very inexperienced in terms of stuff like that. A answer for >>>> dummies would be much appreciated. >>>> Thanks >>>> Christoph >>>> >>>> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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