[BioC] Snp matching

[James W. MacDonald]

Mohamed Lajnef wrote:
> Dear  Martin & Hans,
> 
> gene not gene1 sorry for the mistake! yes i  am sure about this gene  
> (http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=sam),

You shouldn't be sure about it. There are no Homo sapiens entries from 
that search. So you are either using the wrong org.Xx.eg.db package or 
you are looking for the wrong gene symbol.

Adding homo sapiens removes all the SAM entries:

http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=DetailsSearch&Term=sam+AND+homo+sapiens

This search probably returns the gene you are looking for:

http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=DetailsSearch&Term=S-adenosylmethionine+AND+homo+sapiens

Which is where Hans was directing you.

Best,

Jim





> thank you again for your help
> 
> M
> Martin Morgan a écrit :
>> Hotz, Hans-Rudolf wrote:
>>> Hi Mohamed
>>>
>>>
>>> I don't think it is a Bioconductor issue anymore...are you sure about 
>>> the
>>> gene name "SAM"?
>>> I am just guessing: How about "SAMC" or "SLC25A26"
>>>
>>>
>>> Hans
>>>
>>>
>>>
>>>
>>> On 9/29/09 3:11 PM, "Rhoda Kinsella" <rhoda at ebi.ac.uk> wrote:
>>>
>>>> Hi Mohamed,
>>>> I am glad that my suggestion has helped but i'm afraid I am not an
>>>> expert bioconductor user. Perhaps someone else on this mailing list
>>>> has experience with similar queries?
>>>> I hope you find an answer to your query,
>>>> Regards,
>>>> Rhoda
>>>>
>>>>
>>>> On 29 Sep 2009, at 13:59, Mohamed Lajnef wrote:
>>>>
>>>>> Hi Rhoda,
>>>>>
>>>>> thank you for your answer! it works, but among my list of genes  i
>>>>> can not find the gene SAM(sam-adenosylmethionine transporter)  when
>>>>> i used org.Hs.egALIAS2EG mappings .
>>>>>
>>>>> library(org.Hs.eg.db)
>>>>> library("SNPlocs.Hsapiens.dbSNP.20080617")
>>>>> gene<-c("PPP3CC","DNMT1","SMS","SAM","MTHFR")
>>>>> egs <- unlist(mget(gene1, org.Hs.egALIAS2EG))
>>
>> note 'gene1' instead of 'gene'
>>
>> it might be helpful to
>>
>> ids = ls(org.Hs.egALIAS2EG)
>> ids[grepl("SAM", ids)]
>>
>> or
>>
>> nms = ls(revmap(org.Hs.egGENENAME))
>> nms[grepl("adenosylmethionine", nms)]
>>
>> Martin
>>
>>>>>
>>>>>
>>>>> *Error dans .checkKeys(value, Rkeys(x), x at ifnotfound) :
>>>>>   value for "SAM" not found*
>>>>>
>>>>> All suggestions are welcome!
>>>>>
>>>>> Thanks
>>>>>
>>>>>
>>>>> Best
>>>>>
>>>>>
>>>>> M
>>>>>
>>>>>
>>>>> Rhoda Kinsella a écrit :
>>>>>> Hi Mohamed,
>>>>>> I've just had a look at the Bioconductor Changelog
>>>>>> (http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi/biomaRt
>>>>>> ) and there is an entry on 14th Jan 2009 that says:
>>>>>>
>>>>>> biomaRt
>>>>>> Removed getSNP, getHomolog, getAffyArrays as these functions are
>>>>>> replaced by getBM and getLDS
>>>>>>
>>>>>>
>>>>>> So i guess you should try to use getBM or getLDS instead of getSNP.
>>>>>> Regards,
>>>>>> Rhoda
>>>>>>
>>>>>>
>>>>>> On 29 Sep 2009, at 08:47, Mohamed Lajnef wrote:
>>>>>>
>>>>>>> Dear All,
>>>>>>>
>>>>>>> I try to use biomart package to find the snps matching of some
>>>>>>> genes:
>>>>>>> PPP3CC
>>>>>>> DNMT1
>>>>>>> SMS
>>>>>>> PPIEL
>>>>>>> SAM
>>>>>>> MTHFR
>>>>>>> snpmart = useMart("snp", dataset = "hsapiens_snp")  but getSnp
>>>>>>> function does not work and i have this message
>>>>>>> Error:"Can not find function "getSNP", Can someone help me to
>>>>>>> solve this problem?
>>>>>>> Regards
>>>>>>> M
>>>>>>>
>>>>>>>
>>>>>>> -- 
>>>>>>> Mohamed Lajnef
>>>>>>> INSERM Unité 955. 40 rue de Mesly. 94000 Créteil.
>>>>>>> Courriel : Mohamed.lajnef at inserm.fr tel. : 01 49 81 31 31 (poste
>>>>>>> 18470)
>>>>>>> Sec : 01 49 81 32 90
>>>>>>> fax : 01 49 81 30 99
>>>>>>> _______________________________________________
>>>>>>> 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
>>>>>> Rhoda Kinsella Ph.D.
>>>>>> Ensembl Bioinformatician,
>>>>>> European Bioinformatics Institute (EMBL-EBI),
>>>>>> Wellcome Trust Genome Campus,
>>>>>> Hinxton
>>>>>> Cambridge CB10 1SD,
>>>>>> UK.
>>>>>>
>>>>>>
>>>>>
>>>>> -- 
>>>>> Mohamed Lajnef
>>>>> INSERM Unité 955. 40 rue de Mesly. 94000 Créteil.
>>>>> Courriel : Mohamed.lajnef at inserm.fr tel. : 01 49 81 31 31 (poste
>>>>> 18470)
>>>>> Sec : 01 49 81 32 90
>>>>> fax : 01 49 81 30 99
>>>> Rhoda Kinsella Ph.D.
>>>> Ensembl Bioinformatician,
>>>> European Bioinformatics Institute (EMBL-EBI),
>>>> Wellcome Trust Genome Campus,
>>>> Hinxton
>>>> Cambridge CB10 1SD,
>>>> UK.
>>>>
>>>> _______________________________________________
>>>> 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
>>>
>>> _______________________________________________
>>> 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
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826