help with illumina microarray (DASL)
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@taylor-katie-4048
Last seen 8.1 years ago
Hello, I hope that you can help me. I am looking for a way to make a hyperlink table/html document which contains the annotation and data of my illumina microarray. Does anyone know if this can be done? I have found functions where I can look up a range or individual set of genes but I need the whole table. I've been using annaffy for some geo data that I downloaded but I was wondering if somthing like this could also be used for illumina? The nuID conversion is what makes me think that annaffy can't be used but I can't find anything in lumi which will do what I need. I would be really grateful of any help that you could give me. Best Wishes, Katie
Microarray Annotation annaffy lumi Microarray Annotation annaffy lumi • 907 views
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@vincent-j-carey-jr-4
Last seen 23 days ago
United States
you don't say which array you are using so full details can't be provided, but one approach for human arrays is > library(lumiHumanAll.db) Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: org.Hs.eg.db Loading required package: DBI > library(annaffy) Loading required package: GO.db Loading required package: KEGG.db > pr = mappedkeys(lumiHumanAllENTREZID) > length(pr) [1] 46237 # # i find the full mapping is slow, but for 50 probes: # > afm = aafTableAnn(pr[1:50], "lumiHumanAll.db") > saveHTML(afm, file="~/afm.html") # # now point browser to ~/afm.html # > sessionInfo() R version 2.12.0 Under development (unstable) (2010-05-03 r51901) x86_64-apple-darwin10.3.0 locale: [1] C attached base packages: [1] stats graphics grDevices datasets tools utils methods [8] base other attached packages: [1] annaffy_1.21.0 KEGG.db_2.4.1 GO.db_2.4.1 [4] lumiHumanAll.db_1.10.0 org.Hs.eg.db_2.4.1 RSQLite_0.9-0 [7] DBI_0.2-5 AnnotationDbi_1.11.1 Biobase_2.9.0 [10] weaver_1.15.0 codetools_0.2-2 digest_0.4.2 On Mon, May 17, 2010 at 4:31 AM, Taylor, Katie <kt70@leicester.ac.uk> wrote: > Hello, > > I hope that you can help me. I am looking for a way to make a hyperlink > table/html document which contains the annotation and data of my illumina > microarray. Does anyone know if this can be done? I have found functions > where I can look up a range or individual set of genes but I need the whole > table. I've been using annaffy for some geo data that I downloaded but I was > wondering if somthing like this could also be used for illumina? The nuID > conversion is what makes me think that annaffy can't be used but I can't > find anything in lumi which will do what I need. I would be really grateful > of any help that you could give me. > > Best Wishes, > > Katie > _______________________________________________ > 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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Pan Du ★ 1.2k
@pan-du-2010
Last seen 8.1 years ago
Hi Katie As long as you have matched Bioconductor annotation package for your data, you can use annaffy to produce html document. The current lumi annotation packages do not include DASL chips. But you can easily create one by yourself using AnnotationDbi package. BTW, when you input the Illumina data using lumiR, you can easily turn off the nuID conversion by set convertNuID parameter as FALSE. Pan On 5/17/10 11:26 AM, "gilbert feng" <g-feng at="" northwestern.edu=""> wrote: > From: "Taylor, Katie" <kt70 at="" leicester.ac.uk=""> > Date: Mon, 17 May 2010 09:31:02 +0100 > To: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > Conversation: help with illumina microarray (DASL) > Subject: [BioC] help with illumina microarray (DASL) > > Hello, > > I hope that you can help me. I am looking for a way to make a hyperlink > table/html document which contains the annotation and data of my illumina > microarray. Does anyone know if this can be done? I have found functions > where I can look up a range or individual set of genes but I need the whole > table. I've been using annaffy for some geo data that I downloaded but I was > wondering if somthing like this could also be used for illumina? The nuID > conversion is what makes me think that annaffy can't be used but I can't > find anything in lumi which will do what I need. I would be really grateful > of any help that you could give me. > > Best Wishes, > > Katie > _______________________________________________ > 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 > -- Pan Du, PhD Research Assistant Professor Northwestern University Biomedical Informatics Center 750 N. Lake Shore Drive, 11-176 Chicago, IL 60611 Office (312) 503-2360; Fax: (312) 503-5388 dupan (at) northwestern.edu
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