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Question: GSEABase how to map gene symbols to mouse EntrezId or Affy
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gravatar for Vladimir Morozov
9.6 years ago by
Vladimir Morozov130 wrote:
Hi Any suggestions how to map gene symbols to mouse EntrezId(preffered) or Affy. mapping to Entez apparently is not supported by GSEABase > mapIdentifiers(gss,EntrezIdentifier()) Error in .mapIdentifiers_isMappable(from, to) : unable to map from 'Symbol' to 'EntrezId' neither GeneIdentifierType has annotation Error in GeneSetCollection(lapply(what, mapIdentifiers, to, ..., verbose = verbose)) : error in evaluating the argument 'object' in selecting a method for function 'GeneSetCollection' Mapping to Affys works for human, but not for mouse > mapIdentifiers(gss, AnnotationIdentifier("hgu95av2.db")) GeneSetCollection names: chr5q23, chr16q24 (2 total) unique identifiers: 35089_at, 35090_g_at, ..., 35807_at (79 total) types in collection: geneIdType: AnnotationIdentifier (1 total) collectionType: BroadCollection (1 total) > mapIdentifiers(gss, AnnotationIdentifier("mouse4302.db")) GeneSetCollection names: chr5q23, chr16q24 (2 total) unique identifiers: (0 total) types in collection: geneIdType: AnnotationIdentifier (1 total) collectionType: BroadCollection (1 total) > Thanks Vladimir Morozov [[alternative HTML version deleted]]
ADD COMMENTlink modified 9.6 years ago by Marc Carlson7.2k • written 9.6 years ago by Vladimir Morozov130
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gravatar for Marc Carlson
9.6 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Vladimir Morozov wrote: > Hi > > Any suggestions how to map gene symbols to mouse EntrezId(preffered) or > Affy. > mapping to Entez apparently is not supported by GSEABase > Hi Vladimir, In general if you want to map mouse gene symbols to Entrez Gene IDs, I would use the org.Mm.eg.db package like this: #load the package library("org.Mm.eg.db") #you need a some gene symbols to map of course foo = c("Msx2", "Wnt5a", "Shh") #Then just find what these symbols map to mget(foo, org.Mm.egSYMBOL2EG) If you have more exotic gene symbols in your list (often many symbols will map to a single ID), then you can also use the org.Mm.egALIAS2EG mapping to try and recover the gene IDs that may have otherwise been lost. And if you want to map to affy IDs, we probably have a package for that too, but you need to tell us which platform you are using in order for us to make a recommendation. Marc
ADD COMMENTlink written 9.6 years ago by Marc Carlson7.2k
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