Hi Jim,

Thank you very much for the detailed response, that's very helpful.  And
apologies for the delayed response on my part.

Cheers,

_Taku



On Thu, Mar 27, 2014 at 6:38 AM, James W. MacDonald <jmacdon@uw.edu> wrote:

> Hi Taku,
>
> This 'error' is not due to anything in the illuminahumanv4.db package. All
> that package does is link the probe IDs to Entrez Gene IDs, and then the
> org.Hs.eg.db package does the remainder of the annotation. So if we look at
> org.Hs.eg.db, we get this:
>
> > select(org.Hs.eg.db, c("C16ORF15","C16orf15","C15orf16"),
> c("ENTREZID","SYMBOL","GENENAME"), "ALIAS")
>      ALIAS ENTREZID SYMBOL                 GENENAME
> 1 C16ORF15   161725 OTUD7A OTU domain containing 7A
> 2 C16orf15   197335  WDR90      WD repeat domain 90
> 3 C15orf16   161725 OTUD7A OTU domain containing 7A
>
>
> And if we go to NCBI and search the Gene database, we get (in order):
>
> Gene ID 161725
>
> Official Symbol
>    OTUD7Aprovided by HGNC <http://www.genenames.org/>
> Official Full Name
>    OTU deubiquitinase 7Aprovided by HGNC <http://www.genenames.org/>
> Primary source
>    HGNC:20718 <http://www.genenames.org/data/hgnc_data.php?hgnc_id=20718>
> See related
>    Ensembl:ENSG00000169918; <http://www.ensembl.org/id/ENSG00000169918>
>    HPRD:12666; <http://www.hprd.org/protein/12666> MIM:612024;
>    <http://www.ncbi.nlm.nih.gov/omim/612024> Vega:OTTHUMG00000129275
>    <http://vega.sanger.ac.uk/id/OTTHUMG00000129275> Gene type
>    protein coding
> RefSeq status
>    PROVISIONAL
> Organism
>    Homo sapiens
>    <https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9606>
> Lineage
>    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
>    Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
>    Catarrhini; Hominidae; Homo
> Also known as
>    OTUD7; C15orf16; C16ORF15; CEZANNE2
>
> And
>
> Gene ID 197335
>
> Official Symbol
>    WDR90provided by HGNC <http://www.genenames.org/>
> Official Full Name
>    WD repeat domain 90provided by HGNC <http://www.genenames.org/>
> Primary source
>    HGNC:26960 <http://www.genenames.org/data/hgnc_data.php?hgnc_id=26960>
> See related
>    Ensembl:ENSG00000161996; <http://www.ensembl.org/id/ENSG00000161996>
>    HPRD:08311; <http://www.hprd.org/protein/08311> HPRD:14118;
>    <http://www.hprd.org/protein/14118> Vega:OTTHUMG00000048040
>    <http://vega.sanger.ac.uk/id/OTTHUMG00000048040> Gene type
>    protein coding
> RefSeq status
>    PROVISIONAL
> Organism
>    Homo sapiens
>    <https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9606>
> Lineage
>    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
>    Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
>    Catarrhini; Hominidae; Homo
> Also known as
>    C16orf15; C16orf16; C16orf17; C16orf18; C16orf19
>
>
> So what is in the org.Hs.eg.db package conforms exactly to the data from
> NCBI. Please note that the annotation packages supplied by Bioconductor are
> simply re-formulations of data we get from sources like NCBI, and we make
> no claims as to the accuracy of those data. In other words, we try our best
> to ensure that the information you get from a given annotation package
> conforms exactly to what you would get by going to the NCBI website and
> searching by hand, but do NOT make any claims as to the accuracy of the
> data on the NCBI website.
>
> And there have been any number of emails on this list by Marc Carlson,
> explaining to people that HGNC symbols and especially other random aliases
> are not unique, and should not be relied upon for annotating data
> accurately. So yeah, don't do that.
>
> Best,
>
> Jim
>
>
>
> On 3/27/2014 6:11 AM, Taku Tokuyasu wrote:
>
>> Hello Mark,
>>
>> I'm writing to report an apparent error in the illuminaHumanv4.db package,
>> version 1.20.0.  Specifically, the mapping for "C16ORF15" in ALIAS2PROBE
>> appears to be incorrect.  Below is an R code snippet:
>>
>> library("illuminaHumanv4.db")
>> packageVersion("illuminaHumanv4.db")
>> # [1] '1.20.0'
>> #
>> http://www.bioconductor.org/packages/release/data/annotation/html/
>> illuminaHumanv4.db.html
>>
>> # Define some mappings
>> xxAP <- as.list(illuminaHumanv4ALIAS2PROBE)
>> xxS <- as.list(illuminaHumanv4SYMBOL)
>>
>> # Compare these two:
>> xxS[xxAP[["C16ORF15"]]]
>> xxS[xxAP[["C16orf15"]]]
>>
>> # I get:
>> # > xxS[xxAP[["C16ORF15"]]]
>> # $ILMN_1718060
>> # [1] "OTUD7A"
>> # $ILMN_1785146
>> # [1] "OTUD7A"
>> # $ILMN_2298160
>> # [1] "OTUD7A"
>> #
>> # > xxS[xxAP[["C16orf15"]]]
>> # $ILMN_1693042
>> # [1] "WDR90"
>> # $ILMN_1698185
>> # [1] "WDR90"
>>
>> According to HGNC (via DuckDuckGo):
>> OTUD7A (OTU domain containing 7A)
>> Protein-coding gene on human chromosome 15q13.1, also known as *C15orf16*,
>>
>> CEZANNE2, OTU domain containing 7, OTUD7, chromosome 15 open reading frame
>> 16.
>>
>> WDR90 (WD repeat domain 90)
>> Protein-coding gene on human chromosome 16p13.3, also known as *C16orf15*,
>>
>> C16orf16, C16orf17, C16orf18, C16orf19, FLJ36483, KIAA1924, chromosome 16
>> open reading frame 15, chromosome 16 open reading frame 16, chromosome 16
>> open reading frame 17, chromosome 16 open reading frame 18, chromosome 16
>> open reading frame 19.
>>
>> So it appears the ALIAS2PROBE mapping for C16ORF15 is actually for
>> C15orf16.  Indeed,
>> all.equal(xxAP[["C16ORF15"]], xxAP[["C15orf16"]])
>> # [1] TRUE
>>
>> Some questions:
>> 1) Why is there a mapping for both C16orf15 and C16ORF15?
>> 2) Can you make the names for mappings like ALIAS2PROBE all upper case?
>> Perhaps there is a Bioconductor annotation convention that prevents this?
>> 3) I also noticed:
>> nms <- names(xxAP)
>> length(nms); length(unique(nms)); length(unique(toupper(nms)))
>> # [1] 99696
>> # [1] 99696
>> # [1] 99378
>> Is there potentially a problem with the 300-odd names that are no longer
>> unique when raised to upper case?
>>
>> Regards,
>>
>> _Taku
>>
>>   Taku A. Tokuyasu, PhD
>> Computational Biology Core
>> UCSF Helen Diller Family Comprehensive Cancer Center
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>

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