Annotation of hgu133a2 chip from limma

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Pengcheng Lu ▴ 10

@pengcheng-lu-2614

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ADD COMMENT • link updated 16.7 years ago by James W. MacDonald 67k • written 16.7 years ago by Pengcheng Lu ▴ 10

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Marc Carlson ★ 7.2k

@marc-carlson-2264

Last seen 8.2 years ago

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Pengcheng Lu wrote: > Greetings- > > I want to annotate the gene symbols and other gene information for > affy chip hgu133a2. Tried many times but failed. Can you tell me how > I can finish it using limma or other packages in R? > > Thanks, > Pengcheng Lu > [[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 > > Have you tried using the annotation package yet? http://bioconductor.org/packages/2.1/data/annotation/html/hgu133a2.db. html Here is another link to give you some directions about how to use annotation packages in case you are new to this: http://bioconductor.org/packages/bioc/vignettes/annotate/inst/doc/anno tate.pdf But if you have already tried these things, can you please tell me what you have tried so far ( with results to a sessionInfo() in R) ? We even have a posting guide to help you know what sorts of things to put into your post here: http://www.bioconductor.org/docs/postingGuide.html Maybe if I know a little bit more about what you are trying to do I can help you out better. ;) Marc

ADD COMMENT • link 16.7 years ago Marc Carlson ★ 7.2k

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Why don't you use the Gene Annotation tool in EzArray? You don't even need to write any codes. Try it at [1]http://xulab.wisc.edu/ezarray/ (only guest account is allowed). Ron Marc Carlson wrote: Pengcheng Lu wrote: Greetings- I want to annotate the gene symbols and other gene information for affy chip hgu133a2. Tried many times but failed. Can you tell me how I can finish it using limma or other packages in R? Thanks, Pengcheng Lu [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list [2]Bioconductor at stat.math.ethz.ch [3]https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: [4]http://news.gmane.org/gmane.science.biology.informatics .conductor Have you tried using the annotation package yet? [5]http://bioconductor.org/packages/2.1/data/annotation/html/hgu133a2. db.html Here is another link to give you some directions about how to use annotation packages in case you are new to this: [6]http://bioconductor.org/packages/bioc/vignettes/annotate/inst/doc/a nnotate.p df But if you have already tried these things, can you please tell me what you have tried so far ( with results to a sessionInfo() in R) ? We even have a posting guide to help you know what sorts of things to put into your post here: [7]http://www.bioconductor.org/docs/postingGuide.html Maybe if I know a little bit more about what you are trying to do I can help you out better. ;) Marc _______________________________________________ Bioconductor mailing list [8]Bioconductor at stat.math.ethz.ch [9]https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: [10]http://news.gmane.org/gmane.science.biology.informatic s.conductor References 1. http://xulab.wisc.edu/ezarray/ 2. mailto:Bioconductor at stat.math.ethz.ch 3. https://stat.ethz.ch/mailman/listinfo/bioconductor 4. http://news.gmane.org/gmane.science.biology.informatics.conductor 5. http://bioconductor.org/packages/2.1/data/annotation/html/hgu133 a2.db.html 6. http://bioconductor.org/packages/bioc/vignettes/annotate/inst/do c/annotate.pdf 7. http://www.bioconductor.org/docs/postingGuide.html 8. mailto:Bioconductor at stat.math.ethz.ch 9. https://stat.ethz.ch/mailman/listinfo/bioconductor 10. http://news.gmane.org/gmane.science.biology.informatics.conductor

ADD REPLY • link 16.7 years ago Ron ▴ 40

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 13 hours ago

United States

Hi Pengcheng Lu, Pengcheng Lu wrote: > Greetings- > > I want to annotate the gene symbols and other gene information for > affy chip hgu133a2. Tried many times but failed. Can you tell me how > I can finish it using limma or other packages in R? limma is a package for doing linear models, not annotating. To annotate things you can use functions in the annotate package, the hgu133a2.db annotation package directly, the annaffy package, or the affycoretools package. Each of annotate, annaffy, and affycoretools have vignettes that show how to use the packages, so I would start there. Best, Jim > > Thanks, > Pengcheng Lu > [[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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623

ADD COMMENT • link 16.7 years ago James W. MacDonald 67k

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