Question: getting closer on YEAST 2.0 annotation...
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gravatar for Jacob Michaelson
14.7 years ago by
Jacob Michaelson320 wrote:
I've gotten closer to getting a working yeast annotation package for the Affymetrix YEAST 2.0 chip. I was able to procure the proper ORF ids and the probe ids, and from there I used yeastPkgBuilder within AnnBuilder to create a package. It ran for a few hours and terminated with the following error: Error in readLines(con) : cannot open the connection From what I can tell, it got most (if not all) of the probes processed. I tried installing the package from the shell using R CMD INSTALL YEAST2 YEAST2 is the name I gave to the package. I get the error: WARNING: invalid package 'YEAST2' ERROR: no packages specified I know it's there, it just doesn't think the directory is a valid package (dir includes R, man, data subdirectories). I also tired installing via the Mac OS X GUI, which also failed. There was also an XML file made, which seems to contain all the proper annotation. Is there any way to create an annotation package from this XML file? Why even make the XML file? (Just curious). Thanks in advance, Jake Michaelson
annotation gui yeast probe • 620 views
ADD COMMENTlink modified 14.7 years ago by John Zhang2.9k • written 14.7 years ago by Jacob Michaelson320
Answer: getting closer on YEAST 2.0 annotation...
0
gravatar for John Zhang
14.7 years ago by
John Zhang2.9k
John Zhang2.9k wrote:
>I've gotten closer to getting a working yeast annotation package for >the Affymetrix YEAST 2.0 chip. I was able to procure the proper ORF >ids and the probe ids, and from there I used yeastPkgBuilder within >AnnBuilder to create a package. It ran for a few hours and terminated >with the following error: > >Error in readLines(con) : cannot open the connection The code was trying to access a public data source (most likely GO based on the time spent) when the site was probably down. > > From what I can tell, it got most (if not all) of the probes processed. > I tried installing the package from the shell using > >R CMD INSTALL YEAST2 > >YEAST2 is the name I gave to the package. I get the error: > >WARNING: invalid package 'YEAST2' >ERROR: no packages specified Was there a DESCRIPTION file. The build was interrupted and the package may not have all the required elements for a package. > >I know it's there, it just doesn't think the directory is a valid >package (dir includes R, man, data subdirectories). I also tired >installing via the Mac OS X GUI, which also failed. > >There was also an XML file made, which seems to contain all the proper >annotation. Is there any way to create an annotation package from this >XML file? Why even make the XML file? (Just curious). You can set makeXML = FALSE to turn it off. > >Thanks in advance, > >Jake Michaelson > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
ADD COMMENTlink written 14.7 years ago by John Zhang2.9k
On Feb 15, 2005, at 6:52 AM, John Zhang wrote: > >> I've gotten closer to getting a working yeast annotation package for >> the Affymetrix YEAST 2.0 chip. I was able to procure the proper ORF >> ids and the probe ids, and from there I used yeastPkgBuilder within >> AnnBuilder to create a package. It ran for a few hours and terminated >> with the following error: >> >> Error in readLines(con) : cannot open the connection > > The code was trying to access a public data source (most likely GO > based on the > time spent) when the site was probably down. > >> >> From what I can tell, it got most (if not all) of the probes >> processed. >> I tried installing the package from the shell using >> >> R CMD INSTALL YEAST2 >> >> YEAST2 is the name I gave to the package. I get the error: >> >> WARNING: invalid package 'YEAST2' >> ERROR: no packages specified > > Was there a DESCRIPTION file. The build was interrupted and the > package may not > have all the required elements for a package. The following files were created: YEAST2ALIAS.rda YEAST2CHR.rda YEAST2CHRLOC.rda YEAST2DESCRIPTION.rda YEAST2GENENAME.rda YEAST2GO.rda YEAST2ORF.rda YEAST2PMID.rda YEAST2PMID2PROBE.rda > >> >> I know it's there, it just doesn't think the directory is a valid >> package (dir includes R, man, data subdirectories). I also tired >> installing via the Mac OS X GUI, which also failed. >> >> There was also an XML file made, which seems to contain all the proper >> annotation. Is there any way to create an annotation package from >> this >> XML file? Why even make the XML file? (Just curious). > > You can set makeXML = FALSE to turn it off. I know I can turn it off -- I just wanted to know what the purpose would be (within BioC) of making an XML version. > >> >> Thanks in advance, >> >> Jake Michaelson >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor > > Jianhua Zhang > Department of Medical Oncology > Dana-Farber Cancer Institute > 44 Binney Street > Boston, MA 02115-6084 > Jake Michaelson [[alternative text/enriched version deleted]]
ADD REPLYlink written 14.7 years ago by Jacob Michaelson320
Answer: getting closer on YEAST 2.0 annotation...
0
gravatar for John Zhang
14.7 years ago by
John Zhang2.9k
John Zhang2.9k wrote:
>The following files were created: >YEAST2ALIAS.rda >YEAST2CHR.rda >YEAST2CHRLOC.rda >YEAST2DESCRIPTION.rda >YEAST2GENENAME.rda >YEAST2GO.rda >YEAST2ORF.rda >YEAST2PMID.rda >YEAST2PMID2PROBE.rda Looks like KEGG was not available. If the above environments are enough for you, you may write a DESCRIPTION file under YEAST2 and then install the package. > >> >>> >>> I know it's there, it just doesn't think the directory is a valid >>> package (dir includes R, man, data subdirectories). I also tired >>> installing via the Mac OS X GUI, which also failed. >>> >>> There was also an XML file made, which seems to contain all the proper >>> annotation. Is there any way to create an annotation package from >>> this >>> XML file? Why even make the XML file? (Just curious). >> >> You can set makeXML = FALSE to turn it off. > >I know I can turn it off -- I just wanted to know what the purpose >would be (within BioC) of making an XML version. For people who may want to use the annotation data in other platforms. > >> >>> >>> Thanks in advance, >>> >>> Jake Michaelson >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> Jianhua Zhang >> Department of Medical Oncology >> Dana-Farber Cancer Institute >> 44 Binney Street >> Boston, MA 02115-6084 >> > >Jake Michaelson > > [[alternative text/enriched version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
ADD COMMENTlink written 14.7 years ago by John Zhang2.9k
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