[BioC] GO's to gene's

[Martin Morgan]

On 03/01/2010 08:54 PM, Loren Engrav wrote:
> This is fun, least for me

yes it is fun...

> But I am smiling, you want me to write a query? I can barely plagiarize your
> commands.
> 
> Ok I can do this
> 
> You could not find 9697, sobeit.
> You found 1471 so why do I have it missing?  My mistake, it was on the
> previous printout page.
> 
> Ok so I try your method for 3570 and 3091.
> 
>>  names (org.Hs.egGO[["3570"]])
>  [1] "GO:0002384" "GO:0002548" "GO:0002690" "GO:0006953" "GO:0050829"
> "GO:0042981" "GO:0031018"
>  [8] "GO:0031018" "GO:0032722" "GO:0032755" "GO:0034097" "GO:0042517"
> "GO:0045669" "GO:0045768"
> [15] "GO:0048661" "GO:0050731" "GO:0070102" "GO:0070120" "GO:0005886"
> "GO:0016021" "GO:0005576"
> [22] "GO:0005896" "GO:0016324" "GO:0005102" "GO:0004872" "GO:0004897"
> "GO:0004915" "GO:0019899"
> [29] "GO:0042803" "GO:0070119"
> 
> Nope, 0032966 not there. I check Amigo and it is there.
> 
>>  names (org.Hs.egGO[["3091"]])
>  [1] "GO:0001666" "GO:0001755" "GO:0001837" "GO:0001892" "GO:0001938"
> "GO:0001947" "GO:0002248"
>  [8] "GO:0007165" "GO:0006089" "GO:0006355" "GO:0006879" "GO:0010575"
> "GO:0010634" "GO:0014850"
> [15] "GO:0042981" "GO:0046886" "GO:0030154" "GO:0030949" "GO:0032364"
> "GO:0032722" "GO:0032909"
> [22] "GO:0032963" "GO:0035162" "GO:0042541" "GO:0042593" "GO:0042789"
> "GO:0043193" "GO:0043619"
> [29] "GO:0045648" "GO:0045766" "GO:0045821" "GO:0045926" "GO:0045941"
> "GO:0045944" "GO:0046716"
> [36] "GO:0050790" "GO:0051000" "GO:0051216" "GO:0051541" "GO:0005634"
> "GO:0005737" "GO:0005667"
> [43] "GO:0005730" "GO:0009434" "GO:0003705" "GO:0004871" "GO:0008134"
> "GO:0051879" "GO:0035035"
> [50] "GO:0043565" "GO:0046982" "GO:0046982"
> 
> Yup, 0032963 is there, so why missed? So
>> org.Hs.egGO2EG[["GO:0032963"]]
>    IEA    IMP 
> "3091" "7148" 
> And I trimmed IEA. But Amigo indicates the evidence is ISS.
> 
> So we have
> Two not there
> One my mistake and
> One org.Hs.eg.db lists as IEA and Amigo as ISS.
> 
> I suppose since this question can be answered quite easily with Amigo and
> they update Amigo assocdb weekly,  I should just stick with Amigo for
> questions like this.

... I wouldn't want my results to change every week (Sean said every
month?) so I'll stick with Bioconductor ;) Maybe there is a way in Amigo
to go back in time to the same date as the Bioc package? (there is a
time machine in Bioconductor, just use the previous release(s) of R / Bioc).

> But R/BioC is more fun. And once you have the commands
> in the R.app history, redoing the event is painless, sort of.

Capture your well-trod path into a function, and 'source' it when you
need to; it really will be painless. Here's my (untested) understanding
of what you're after, taken from the various pieces in the email...

getGo <-
    function(likeTerm, inOntology, excludeEvidence)
{
    require(GO.db)
    require(org.Hs.eg.db)

    terms <- Term(GOTERM)
    ontologies <- Ontology(GOTERM)

    idx <- grepl(likeTerm, terms) & (inOntology == ontologies)
    myterms <- terms[idx]

    egids <- mget(names(myterms), org.Hs.egGO2EG, ifnotfound=NA)
    egids <- lapply(egids, function(elt)  {
        ok <- !(names(elt) %in% excludeEvidence)
        elt[ok]
    })
    egids[!sapply(egids, length) == 0]
}

Using the suggestion from Vince to make direct SQL quries might make
this _really_ fun.

Martin

> 
> Again, thank you.
> 
> 
>> From: Martin Morgan <mtmorgan at fhcrc.org>
>> Date: Mon, 01 Mar 2010 19:49:05 -0800
>> To: Loren Engrav <engrav at u.washington.edu>
>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
>> Subject: Re: [BioC] GO's to gene's
>>
>> On 03/01/2010 06:34 PM, Loren Engrav wrote:
>>> Thank you
>>> You are clearly very good at this
>>>
>>> So to check it all out I did it manually on Amigo. Amigo found 33 genes
>>> (limited to Human and omitting IEA)
>>>
>>> The org.HS.eg.db method found 29 of the 33 but did not find
>>> CST3 (1471) GO:0010711 IEP
>>> HIF1A (3091) GO:0032963 ISS
>>> IL6R (3570), GO:0032966 IDA and
>>> TRAM2 (9697) GO:0032964 IMP
>>>
>>> I suppose to figure out, for example, why org.Hs.eg.db does not map 9697 to
>>> GO:0032964 is complex
>>
>>> names(org.Hs.egGO[["9697"]])
>> [1] "GO:0015031" "GO:0065002" "GO:0016020" "GO:0016021"
>>
>> Hmm, what are the offspring / ancestors of GO:0032964 ?
>>
>>> GOBPOFFSPRING[["GO:0032964"]]
>> [1] "GO:0032965" "GO:0032966" "GO:0032967"
>>> GOBPANCESTOR[["GO:0032964"]]
>>  [1] "all"        "GO:0008152" "GO:0008150" "GO:0009058" "GO:0009059"
>>  [6] "GO:0032501" "GO:0032963" "GO:0043170" "GO:0044236" "GO:0044259"
>>
>> Nope nothing jumping out. Where's the GO data coming from?
>>
>>> org.Hs.eg() ## or GO()
>> [snip]
>> Date for GO data: 20090830
>>
>> Whereas AMIGO says (at the bottom of each page)
>>
>>   GO database release 2010-02-27
>>
>> so that looks like a likely issue that would require some more
>> substantial investigation. Merits of using a 'current' db (Amigo) vs a
>> 'versioned' db (GO.db)? See mailing list archives, e.g., current
>> state-of-knowledge vs. reproducibility (how would we redo the analysis
>> we did last month and get the same results with AMIGO?).
>>
>> On the other hand
>>
>>> org.Hs.egGO2EG[["GO:0010711"]]
>>    IEP
>> "1471"
>>> GOTERM[["GO:0010711"]]
>> GOID: GO:0010711
>> Term: negative regulation of collagen catabolic process
>> Ontology: BP
>> Definition: Any process that decreases the rate, frequency or extent of
>>     collagen catabolism. Collagen catabolism is the proteolytic
>>     chemical reactions and pathways resulting in the breakdown of
>>     collagen in the extracellular matrix.
>> Synonym: down regulation of collagen catabolic process
>> Synonym: down-regulation of collagen catabolic process
>> Synonym: downregulation of collagen catabolic process
>> Synonym: inhibition of collagen catabolic process
>> Synonym: negative regulation of collagen breakdown
>> Synonym: negative regulation of collagen catabolism
>> Synonym: negative regulation of collagen degradation
>>
>> so why didn't we find that one?
>>
>>> terms <- Term(GOTERM)  # or maybe Definition(GOTERM)
>>> "GO:0010711" %in% names(terms)
>> [1] TRUE
>>> terms[["GO:0010711"]]
>> [1] "negative regulation of collagen catabolic process"
>>
>> yep it's there
>>
>>> ontologies <- Ontology(GOTERM)
>>> ontologies[["GO:0010711"]]
>> [1] "BP"
>>> collagen <- terms[grepl("collagen", terms) & ("BP" == ontologies)]
>>> collagen[["GO:0010711"]]
>> [1] "negative regulation of collagen catabolic process"
>>
>> yep it's there (or were we looking for MF, as below?).
>>
>>> egids[["GO:0010711"]]
>>    IEP
>> "1471"
>>
>> yep it's there. So this makes me think it's a programming error or a
>> miscommunication. I'd suggest you write a little function
>>
>> getGO <-
>>     function(termLike, ontology, exludeEvidence)
>> {
>>     ## a few lines of code here, representing the query you perform
>> }
>>
>> and perhaps sharing that with the list will shed some light.
>>
>> Martin
>>
>>
>>>
>>> Thank you
>>>
>>>
>>>> From: Martin Morgan <mtmorgan at fhcrc.org>
>>>> Date: Mon, 01 Mar 2010 05:16:48 -0800
>>>> To: Loren Engrav <engrav at u.washington.edu>
>>>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
>>>> Subject: Re: [BioC] GO's to gene's
>>>>
>>>> On 02/28/2010 09:01 PM, Loren Engrav wrote:
>>>>> So I checked
>>>>>> collagen
>>>>> And this list matches Amigo
>>>>> So then would appear the issue lies in
>>>>>> egids <- mget(names(collagen), org.Hs.egGO2EG, ifnotfound=NA)
>>>>> Some of the names are finding no associated genes in org.Hs.egGO2EG and so
>>>>> appear as NA
>>>>> True? Possible?
>>>>
>>>> yes. GO is not H. sapiens specific and ENTREZ ids are not 100%
>>>> comprehensive, so some GO terms do not map to ENTREZ ids.
>>>>
>>>>>>> Also I would like to omit the IEA group
>>>>
>>>> maybe
>>>>
>>>>   egids <- lapply(egids, function(elt)  elt[names(elt) != "IEA"])
>>>>   egids[sapply(egids, length) != 0]
>>>>
>>>> Martin
>>>>
>>>>> My version of org.Hs.egGO2EG is 2.3.6
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> From: Loren Engrav <engrav at u.washington.edu>
>>>>>> Date: Sun, 28 Feb 2010 20:33:05 -0800
>>>>>> To: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
>>>>>> Conversation: [BioC] GO's to gene's
>>>>>> Subject: Re: [BioC] GO's to gene's
>>>>>>
>>>>>> Oopps, Amigo says there are 20 such terms, not 68 as I said before, cuz I
>>>>>> retrieved only BP
>>>>>>
>>>>>>
>>>>>>> From: Loren Engrav <engrav at u.washington.edu>
>>>>>>> Date: Sun, 28 Feb 2010 20:28:17 -0800
>>>>>>> To: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
>>>>>>> Conversation: [BioC] GO's to gene's
>>>>>>> Subject: Re: [BioC] GO's to gene's
>>>>>>>
>>>>>>> Ok thank you
>>>>>>> I now show
>>>>>>>> sessionInfo()
>>>>>>> R version 2.10.1 (2009-12-14)
>>>>>>> i386-apple-darwin9.8.0
>>>>>>>
>>>>>>> locale:
>>>>>>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>>>>>>
>>>>>>> attached base packages:
>>>>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>>>>
>>>>>>> other attached packages:
>>>>>>> [1] org.Hs.eg.db_2.3.6  GO.db_2.3.5         RSQLite_0.8-3
>>>>>>> AnnotationDbi_1.8.1 DBI_0.2-5
>>>>>>> [6] Biobase_2.6.1
>>>>>>>
>>>>>>> loaded via a namespace (and not attached):
>>>>>>> [1] tools_2.10.1
>>>>>>>
>>>>>>> And all commands pass with no errors, however I see
>>>>>>>
>>>>>>>> egids
>>>>>>> $`GO:0010711`
>>>>>>>    IEP 
>>>>>>> "1471" 
>>>>>>>
>>>>>>> $`GO:0030199`
>>>>>>>     IEA     IEA     ISS     IEA     IMP     IMP     IMP     IMP     NAS
>>>>>>> IMP     NAS     IMP     ISS
>>>>>>>   "302"   "304"   "538"   "871"  "1277"  "1278"  "1280"  "1281"  "1281"
>>>>>>> "1289"  "1289"  "1290"  "1290"
>>>>>>>     NAS     IDA     NAS     IEA     IEA     IEA     IEA     IEA     NAS
>>>>>>> ISS     IDA     ISS     NAS
>>>>>>>  "1301"  "1302"  "1303"  "1805"  "2296"  "2303"  "4010"  "4015"  "4060"
>>>>>>> "4763"  "7042"  "7046"  "7373"
>>>>>>>     NAS     NAS
>>>>>>>  "9508" "50509"
>>>>>>>
>>>>>>> $`GO:0030574`
>>>>>>>      IEA      IEA      IEA      IEA      IEA      IEA      IEA      IEA
>>>>>>> IEA      IEA      IEA
>>>>>>>   "4312"   "4313"   "4314"   "4316"   "4317"   "4318"   "4319"   "4320"
>>>>>>> "4322"   "4325"   "4327"
>>>>>>>      IEA      IDA      IMP      NAS      IEA      NAS      IEA      IEA
>>>>>>> IEA      IEA
>>>>>>>   "5184"   "5645"   "5645"   "5653"   "5657"   "9508"   "9509"  "56547"
>>>>>>> "64066" "140766"
>>>>>>>
>>>>>>> $`GO:0032963`
>>>>>>>    IEA    IMP
>>>>>>> "3091" "7148"
>>>>>>>
>>>>>>> $`GO:0032964`
>>>>>>>    IEA    IMP    IMP    TAS    IMP
>>>>>>>  "871" "1277" "1281" "1281" "1289"
>>>>>>>
>>>>>>> $`GO:0032966`
>>>>>>>    IDA     IC
>>>>>>> "3569" "4261"
>>>>>>>
>>>>>>> $`GO:0032967`
>>>>>>>    ISS    IDA    IDA     IC    IMP    TAS    IMP
>>>>>>>  "265" "2147" "2149" "3066" "7040" "7040" "7043"
>>>>>>>
>>>>>>> $`GO:0033342`
>>>>>>>     IMP 
>>>>>>> "23560"
>>>>>>>
>>>>>>> So many GO terms containing the word "collagen" are not listed, like
>>>>>>> 0004656
>>>>>>> 0005518
>>>>>>> etc
>>>>>>> Amigo claims there are 68 such terms and the list above has only 8
>>>>>>> What did I do wrong?
>>>>>>> Also I would like to omit the IEA group
>>>>>>>
>>>>>>> Thank you
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> From: Martin Morgan <mtmorgan at fhcrc.org>
>>>>>>>> Date: Sun, 28 Feb 2010 19:30:34 -0800
>>>>>>>> To: Loren Engrav <engrav at u.washington.edu>
>>>>>>>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
>>>>>>>> Subject: Re: [BioC] GO's to gene's
>>>>>>>>
>>>>>>>> On 02/28/2010 07:17 PM, Loren Engrav wrote:
>>>>>>>>> Thank you both
>>>>>>>>> Given my skills, it might be easier/quicker to do it "manually" with
>>>>>>>>> Amigo
>>>>>>>>> But I am trying both methods
>>>>>>>>>
>>>>>>>>> For the second method I get
>>>>>>>>>
>>>>>>>>>> library(GO.db)
>>>>>>>>> Loading required package: AnnotationDbi
>>>>>>>>> Loading required package: Biobase
>>>>>>>>>
>>>>>>>>> Welcome to Bioconductor
>>>>>>>>>
>>>>>>>>>   Vignettes contain introductory material. To view, type
>>>>>>>>>   'openVignette()'. To cite Bioconductor, see
>>>>>>>>>   'citation("Biobase")' and for packages 'citation(pkgname)'.
>>>>>>>>>
>>>>>>>>> Loading required package: DBI
>>>>>>>>>> terms <- Term(GOTERM)
>>>>>>>>> Error in function (classes, fdef, mtable)  :
>>>>>>>>>   unable to find an inherited method for function "Term", for signature
>>>>>>>>> "GOTermsAnnDbBimap"
>>>>>>>>>
>>>>>>>>>> sessionInfo()
>>>>>>>>> R version 2.9.2 Patched (2009-09-05 r49613)
>>>>>>>>> i386-apple-darwin9.8.0
>>>>>>>>>
>>>>>>>>> locale:
>>>>>>>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>>>>>>> ,
>>>>>>>>> attached base packages:
>>>>>>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>>>>>
>>>>>>>> Update to R version 2.10 and associated Bioc packages, or for a (much)
>>>>>>>> slower solution (you'll want to check that Term and Ontology return ids
>>>>>>>> in identical order)
>>>>>>>>
>>>>>>>>   terms = eapply(GOTERM, Term)
>>>>>>>>
>>>>>>>> etc. I have
>>>>>>>>
>>>>>>>>> sessionInfo()
>>>>>>>> R version 2.10.1 Patched (2010-02-23 r51168)
>>>>>>>> x86_64-unknown-linux-gnu
>>>>>>>>
>>>>>>>> locale:
>>>>>>>>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>>>>>>>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>>>>>>>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>>>>>>>>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>>>>>>>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>>>>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>>>>>>
>>>>>>>> attached base packages:
>>>>>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>>>>>
>>>>>>>> other attached packages:
>>>>>>>> [1] GO.db_2.3.5         RSQLite_0.7-3       DBI_0.2-4
>>>>>>>> [4] AnnotationDbi_1.8.1 Biobase_2.6.1
>>>>>>>>
>>>>>>>> loaded via a namespace (and not attached):
>>>>>>>> [1] tools_2.10.1
>>>>>>>>
>>>>>>>>
>>>>>>>> Martin
>>>>>>>>
>>>>>>>>>
>>>>>>>>>> From: Martin Morgan <mtmorgan at fhcrc.org>
>>>>>>>>>> Date: Sun, 28 Feb 2010 18:42:33 -0800
>>>>>>>>>> To: Vincent Carey <stvjc at channing.harvard.edu>
>>>>>>>>>> Cc: Loren Engrav <engrav at u.washington.edu>,
>>>>>>>>>> "bioconductor at stat.math.ethz.ch"
>>>>>>>>>> <bioconductor at stat.math.ethz.ch>
>>>>>>>>>> Subject: Re: [BioC] GO's to gene's
>>>>>>>>>>
>>>>>>>>>> On 02/28/2010 06:14 PM, Vincent Carey wrote:
>>>>>>>>>>> Perhaps there is a package with such functionality.  However, with
>>>>>>>>>>> the
>>>>>>>>>>> GO.db package in place, you need to do a little
>>>>>>>>>>> programming, perhaps along the lines of
>>>>>>>>>>>
>>>>>>>>>>> querGO = function(str, attr = "definition", ont = "MF") {
>>>>>>>>>>>   require(GO.db, quietly = TRUE)
>>>>>>>>>>>   gc = GO_dbconn()
>>>>>>>>>>>   quer.1 = paste("select go_id, term from go_term where",
>>>>>>>>>>>   attr, "like('%")
>>>>>>>>>>>   quer.2 = "%') and ontology = '"
>>>>>>>>>>>   quer.3 = "'"
>>>>>>>>>>>   quer = paste(quer.1, str, quer.2, ont, quer.3, collapse = "",
>>>>>>>>>>>   sep = "")
>>>>>>>>>>>   dbGetQuery(gc, quer)
>>>>>>>>>>> }
>>>>>>>>>>>
>>>>>>>>>>> whereby
>>>>>>>>>>>
>>>>>>>>>>>> querGO("collagen", "term")
>>>>>>>>>>>        go_id
>>>>>>>>>>> term
>>>>>>>>>>> 1 GO:0004656                     procollagen-proline 4-dioxygenase
>>>>>>>>>>> activity
>>>>>>>>>>> 2 GO:0005518                                               collagen
>>>>>>>>>>> binding
>>>>>>>>>>> 3 GO:0008475                      procollagen-lysine 5-dioxygenase
>>>>>>>>>>> activity
>>>>>>>>>>> 4 GO:0019797                     procollagen-proline 3-dioxygenase
>>>>>>>>>>> activity
>>>>>>>>>>> 5 GO:0019798                       procollagen-proline dioxygenase
>>>>>>>>>>> activity
>>>>>>>>>>> 6 GO:0033823                       procollagen glucosyltransferase
>>>>>>>>>>> activity
>>>>>>>>>>> 7 GO:0042329 structural constituent of collagen and cuticulin-based
>>>>>>>>>>> cuticle
>>>>>>>>>>> 8 GO:0050211                     procollagen galactosyltransferase
>>>>>>>>>>> activity
>>>>>>>>>>> 9 GO:0070052                                             collagen V
>>>>>>>>>>> binding
>>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Also
>>>>>>>>>>
>>>>>>>>>>   library(GO.db)
>>>>>>>>>>   terms <- Term(GOTERM)  # or maybe Definition(GOTERM) ?
>>>>>>>>>>   ontologies <- Ontology(GOTERM)
>>>>>>>>>>   collagen <- terms[grepl("collagen", terms) & ("MF" == ontologies)]
>>>>>>>>>>
>>>>>>>>>> and the next step,
>>>>>>>>>>
>>>>>>>>>>   library(org.Hs.eg.db)
>>>>>>>>>>   egids <- mget(names(collagen), org.Hs.egGO2EG, ifnotfound=NA)
>>>>>>>>>>   egids <- egids[!is.na(egids)]
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Sun, Feb 28, 2010 at 8:56 PM, Loren Engrav
>>>>>>>>>>> <engrav at u.washington.edu>
>>>>>>>>>>> wrote:
>>>>>>>>>>>> Is there a BioC package that will find all the GO terms containing
>>>>>>>>>>>> some
>>>>>>>>>>>> word, like perhaps ³collagen²
>>>>>>>>>>>> And then find all the genes contained within those found terms
>>>>>>>>>>>>
>>>>>>>>>>>> I scanned
>>>>>>>>>>>> GoProfiles
>>>>>>>>>>>> GOSemSim
>>>>>>>>>>>> GOstats
>>>>>>>>>>>> GoTools and
>>>>>>>>>>>> TopGO
>>>>>>>>>>>>
>>>>>>>>>>>> And could not determine that any would do that.
>>>>>>>>>>>>
>>>>>>>>>>>> Thank you.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>        [[alternative HTML version deleted]]
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> 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
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> -- 
>>>>>>>>>> Martin Morgan
>>>>>>>>>> Computational Biology / Fred Hutchinson Cancer Research Center
>>>>>>>>>> 1100 Fairview Ave. N.
>>>>>>>>>> PO Box 19024 Seattle, WA 98109
>>>>>>>>>>
>>>>>>>>>> Location: Arnold Building M1 B861
>>>>>>>>>> Phone: (206) 667-2793
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> 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
>>>>>>>>
>>>>>>>>
>>>>>>>> -- 
>>>>>>>> Martin Morgan
>>>>>>>> Computational Biology / Fred Hutchinson Cancer Research Center
>>>>>>>> 1100 Fairview Ave. N.
>>>>>>>> PO Box 19024 Seattle, WA 98109
>>>>>>>>
>>>>>>>> Location: Arnold Building M1 B861
>>>>>>>> Phone: (206) 667-2793
>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>>
>>>>
>>>> -- 
>>>> Martin Morgan
>>>> Computational Biology / Fred Hutchinson Cancer Research Center
>>>> 1100 Fairview Ave. N.
>>>> PO Box 19024 Seattle, WA 98109
>>>>
>>>> Location: Arnold Building M1 B861
>>>> Phone: (206) 667-2793
>>>
>>> _______________________________________________
>>> 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
>>
>>
>> -- 
>> Martin Morgan
>> Computational Biology / Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
>> PO Box 19024 Seattle, WA 98109
>>
>> Location: Arnold Building M1 B861
>> Phone: (206) 667-2793
> 
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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 M1 B861
Phone: (206) 667-2793