Re: GSEABase how to map gene symbols to mouse EntrezId or Affy

Martin,

You are right that disagreement beween human and mouse symblos is the
problem. But you still should get some mapping if translate symbols into
capwords
> sum(!is.na(mget(gss[[1]]@geneIds,org.Mm.egSYMBOL2EG,ifnotfound=NA)))
[1] 0
>
sum(!is.na(mget(capwords(tolower(gss[[1]]@geneIds)),org.Mm.egSYMBOL2EG,i
fnotfound=NA)))
[1] 46
Let's say I will figure out some mapping using ortholog or alias names.
Will I screw the GeneSet data structure by
gss2 <- lapply(gss,function(x){x <at> geneIds <-
my.mapping(x <at> geneIds);x <at> geneIdType <at> type <- 'EntrezIdentifier'})
?

Vladimir Morozov 

-----Original Message-----
From: Martin Morgan [mailto:mtmorgan@...] 
Sent: Thursday, May 15, 2008 12:56 PM
To: Vladimir Morozov
Cc: bioconductor@...
Subject: Re: [BioC] GSEABase how to map gene symbols to mouse EntrezId
or Affy

Hi Vladimir --

"Vladimir Morozov" <vmorozov@...> writes:

> 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

mapIdentifiers needs to know where to look for the map. I guess the way
you created gss means that it doesn't know about the organism you're
using, and EntrezIdentifier() also doesn't. What you want is

> mapIdentifiers(gss, EntrezIdentifier("org.Mm.eg.db"))
GeneSetCollection
  names: chr5q23, chr16q24 (2 total)
  unique identifiers:  (0 total)
  types in collection:
    geneIdType: EntrezIdentifier (1 total)
    collectionType: BroadCollection (1 total)

Here I'm using (and I guess you are too) the gss that comes from
example(getBroadSets). These are human genes, and have no corresponding
mouse equivalents (see below)...

> 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)

This is becaus the identifiers are not in mouse

> ids <- unique(unlist(geneIds(gss)))
> egs <- mget(ids, revmap(mouse4302ENTREZID), ifnotfound=NA) 
> sum(!sapply(egs, is.na))
[1] 0

>> 
>  
>  
> Thanks
>  
>
> Vladimir Morozov
>
>
> 	[[alternative HTML version deleted]]
>
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--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center 1100
Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793

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