From KEGG pathways to Affy ProbeID

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Sharon Anbu ▴ 480

@sharon-anbu-1524

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ADD COMMENT • link updated 18.4 years ago by Andrej Kastrin ▴ 90 • written 18.4 years ago by Sharon Anbu ▴ 480

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John Zhang ★ 2.9k

@john-zhang-6

Last seen 9.7 years ago

>I am trying to get Affy ProbeID for all the pathways (particularly for >"rat") in KEGG. I have found a way to do this using >contents(KEGGPATHID2NAME) environment and by using grep to match a >particular pathway. I have to do this step manually for all the pathways. Is >there any other ways to extract affy probeids for corresponding pathways? Is this what you want to do (using rgu34a as an example)? >library(rgu34a) >library(KEGG) >rat34a <- as.list(rgu34aPATH2ID) >names(rat34a) <- unlist(mget(names(rat34a), KEGGPATHID2NAME)) >rat34a[1] $"Propanoate metabolism" [1] "J03621_at" "U75393_s_at" "AB004329_at" ... ... > >Thank you very much in advance. > >Regards, >Sharon > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at 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 COMMENT • link 18.4 years ago John Zhang ★ 2.9k

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ADD REPLY • link 18.4 years ago weinong han ▴ 270

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On 12/29/05 7:24 PM, "weinong han" <hanweinong at="" yahoo.com=""> wrote: > Hi, lists, > > Happy New Year! > > I have different gene lists from three microarray platforms. Now, I want to > match the probes from the three platforms by using accession numbers or by > using Unigene Cluster ID and gene names provided by Affymetrix(HG- U133A and > HG-U95av2) and Operon Technologies(Cologne,Germany), and then map them to the > current version of the UniGene database. > > How to run the procdure? Any advice and suggestions will be much > appreciated. There isn't necessarily a "procedure". You could use the genbank accession numbers from the three arrays as input to stanford Source to get a mapping to recent unigene build. You could also use the annotation packages from Bioconductor to do the same thing, though I'm not sure what operon set you are using and whether there is an annotation package available for it. Once you have each array mapped to a common identifier, you can use the functions "match", "intersect", "union", and "%in%" to determine overlaps in the different sets. Sean

ADD REPLY • link 18.4 years ago Sean Davis 21k

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Andrej Kastrin ▴ 90

@andrej-kastrin-1515

Last seen 9.7 years ago

Sharon Anbu wrote: >Hi All, > >I am trying to get Affy ProbeID for all the pathways (particularly for >"rat") in KEGG. I have found a way to do this using >contents(KEGGPATHID2NAME) environment and by using grep to match a >particular pathway. I have to do this step manually for all the pathways. Is >there any other ways to extract affy probeids for corresponding pathways? > >Thank you very much in advance. > >Regards, >Sharon > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Try with apply() Cheers, Andrej

ADD COMMENT • link 18.4 years ago Andrej Kastrin ▴ 90

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