Question: error msg for probe match (altcdfenvs)
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gravatar for Jack Luo
9.1 years ago by
Jack Luo410
Jack Luo410 wrote:
Hi, I am new to the probe match package altcdfenvs, when I was trying the code from the link: http://127.0.0.1:21417/library/altcdfenvs/html/matchAffyProbes.html library(hgu133aprobe) filename <- system.file("exampleData", "sample.fasta", package="altcdfenvs") fasta.seq <- readFASTA(filename) targets <- unlist(lapply(fasta.seq, "[[", "seq")) names(targets) <- lapply(fasta.seq, "[[", "desc") names(targets) <- sub("^>.+\\|(NM[^ \\|]+|Hs[^ \\|]+)\\| ? .+$", "", names(targets)) m <- matchAffyProbes(hgu133aprobe, targets, "HG-U133A") The error msg is Error in validObject(.Object) : invalid class "AffyProbesMatch" object: labels should be unique. Any idea what's the problem? Thanks, -Jack [[alternative HTML version deleted]]
probe altcdfenvs • 429 views
ADD COMMENTlink modified 9.1 years ago by Laurent Gautier2.2k • written 9.1 years ago by Jack Luo410
Answer: error msg for probe match (altcdfenvs)
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gravatar for Laurent Gautier
9.1 years ago by
Laurent Gautier2.2k
Laurent Gautier2.2k wrote:
On 28/10/10 23:48, Jack Luo wrote: > Hi, > > I am new to the probe match package altcdfenvs, when I was trying the code > from the link: > > http://127.0.0.1:21417/library/altcdfenvs/html/matchAffyProbes.html > > library(hgu133aprobe) > > filename<- system.file("exampleData", "sample.fasta", > package="altcdfenvs") > > fasta.seq<- readFASTA(filename) > > targets<- unlist(lapply(fasta.seq, "[[", "seq")) > names(targets)<- lapply(fasta.seq, "[[", "desc") > names(targets)<- sub("^>.+\\|(NM[^ \\|]+|Hs[^ \\|]+)\\| ? .+$", "", > names(targets)) > > m<- matchAffyProbes(hgu133aprobe, > targets, > "HG-U133A") > > > The error msg is > Error in validObject(.Object) : > invalid class "AffyProbesMatch" object: labels should be unique. > > Any idea what's the problem? A guess: You have sum(duplicated(names(targets))) > 0 And this is obviously not something you want. Laurent > Thanks, > > -Jack > > [[alternative HTML version deleted]] > > _______________________________________________ > 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
ADD COMMENTlink written 9.1 years ago by Laurent Gautier2.2k
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