problem with 2.0 cdf
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@alberto-goldoni-3477
Last seen 9.6 years ago
Dear all, I have 15 cel file and all is good until i try to normalize the dataset: data.rma<rma(data) error="" in="" getcdfinfo(object)="" :="" could="" not="" obtain="" cdf="" environment,="" problems="" encountered:="" specified="" environment="" does="" not="" contain="" 2.0="" library="" -="" package="" 2.0cdf="" not="" installed="" bioconductor="" -="" 2.0cdf="" not="" available=""> data AffyBatch object size of arrays=1164x1164 features (9 kb) cdf=2.0 (??? affyids) number of samples=15 Errore in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain 2.0 Library - package 2.0cdf not installed Bioconductor - 2.0cdf not available why it gives to me this kind of error? I'm using HG-U133_Plus_2_1_1.CEL file and the package hgu133plus2, hgu133plus2cdf and hgu133plus2probe are correctly installed. Someone can help me? Best regards. -- ----------------------------------------------------- Dr. Alberto Goldoni Bologna, Italy ----------------------------------------------------- [[alternative HTML version deleted]]
hgu133plus2 cdf hgu133plus2 cdf • 1.5k views
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@joern-toedling-3465
Last seen 9.6 years ago
Hello, how are you reading in the cel-files? The functions ReadAffy or read.affybatch from package "affy" normally should be able to determine the microarray type and set the cdfName slot of the AffyBatch object correctly. Both also have an argument 'cdfName' which can be used to specify alternative CDF environments. So a dirty hack to "repair" your AffyBatch object would be specifying data at cdfName <- "hgu133plus2" However, I think you should investigate why that information was not in your AffyBatch in the first place. And please always specify the sessionInfo() output when asking questions to this list, such that the maintainers of package "affy" can see which version of the package you are using. Regards, Joern On Fri, 10 Jul 2009 12:57:43 +0200, Alberto Goldoni wrote > Dear all, > > I have 15 cel file and all is good until i try to normalize the dataset: > > data.rma<rma(data)> > Error in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain 2.0 > Library - package 2.0cdf not installed > Bioconductor - 2.0cdf not available > > > data > AffyBatch object > size of arrays=1164x1164 features (9 kb) > cdf=2.0 (??? affyids) > number of samples=15 > Errore in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain 2.0 > Library - package 2.0cdf not installed > Bioconductor - 2.0cdf not available > > why it gives to me this kind of error? > I'm using HG-U133_Plus_2_1_1.CEL file and the package hgu133plus2, > hgu133plus2cdf and hgu133plus2probe are correctly installed. > > Someone can help me? > > Best regards. > > -- > ----------------------------------------------------- > Dr. Alberto Goldoni > Bologna, Italy > -----------------------------------------------------
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@joern-toedling-3465
Last seen 9.6 years ago
Hello, please keep this correspondence on the BioC list for allowing other people to contribute and to have them in the searchable archive. My suggested "hack" was meant as a reply to your source code that did not work, so I assumed there already is an AffyBatch object called 'data'. If you don't have such an object, 'data' will refer to a basic R function with that name. This is the reason why 'data' is actually not a good name for your object. So in detail, my suggestion was to create a working AffyBatch object, for example named 'A', from your CEL files by either A <- ReadAffy(<other arguments,="" see="" ?readaffy="">, cdfName="hgu133plus2") # or by first creating an AffyBatch object by any other way you prefer: A <- ... stopifnot(inherits(A, "AffyBatch")) A@cdfName <- "hgu133plus2" The first way is usually preferable. Regards, Joern PS: when you provide sessionInfo() output, please provide the full output, as we need to know the version of R and the versions of all attached packages. On Fri, 10 Jul 2009 13:58:05 +0200, Alberto Goldoni wrote > i have tryed but with no success > > data@cdfName <- "hgu133plus2" > Error in checkSlotAssignment(object, name, value) : >   "cdfName" is not a slot in class "function" > > > sessionInfo() > R version 2.9.1 (2009-06-26) > i486-pc-linux-gnu > > 2009/7/10 Joern Toedling <joern.toedling@curie.fr> > Hello, > > how are you reading in the cel-files? The functions ReadAffy or read.affybatch > from package "affy" normally should be able to determine the microarray type > and set the cdfName slot of the AffyBatch object correctly. Both also have an > argument 'cdfName' which can be used to specify alternative CDF environments. > > So a dirty hack to "repair" your AffyBatch object would be specifying > data@cdfName <- "hgu133plus2" > > However, I think you should investigate why that information was not in your > AffyBatch in the first place. > > And please always specify the sessionInfo() output when asking questions to > this list, such that the maintainers of package "affy" can see which version > of the package you are using. > > Regards, > Joern > > On Fri, 10 Jul 2009 12:57:43 +0200, Alberto Goldoni wrote > > > Dear all, > > > > I have 15 cel file and all is good until i try to normalize the dataset: > > > > data.rma<rma(data)> > > > Error in getCdfInfo(object) : > >   Could not obtain CDF environment, problems encountered: > > Specified environment does not contain 2.0 > > Library - package 2.0cdf not installed > > Bioconductor - 2.0cdf not available > > > > > data > > AffyBatch object > > size of arrays=1164x1164 features (9 kb) > > cdf=2.0 (??? affyids) > > number of samples=15 > > Errore in getCdfInfo(object) : > >   Could not obtain CDF environment, problems encountered: > > Specified environment does not contain 2.0 > > Library - package 2.0cdf not installed > > Bioconductor - 2.0cdf not available > > > > why it gives to me this kind of error? > > I'm using HG-U133_Plus_2_1_1.CEL file and the package hgu133plus2, > > hgu133plus2cdf and hgu133plus2probe are correctly installed. > > > > Someone can help me? > > > > Best regards. > > > > -- > > ----------------------------------------------------- > > Dr. Alberto Goldoni > > Bologna, Italy [[alternative HTML version deleted]]
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