[BioC] Appropriate Probe annotation for HT-HGU133A chips

[Marc Carlson]

Hi Hannah,

Just to alleviate the confusion that these "ht-hgu133" packages cause
for everyone I have just made an hthgu133a.db
<http://www.bioconductor.org/packages/devel/data/annotation/html/hthgu133a.db.html>
package.  So you can use that.


  Marc


Tipney, Hannah wrote:
> Thank you so much for your quick answers!
> Just so I'm sure I understand for the ht-hgu133a chip I use hgu133a2.db even though I use hthgu133acdf and hthgu133aprobe. Why not the hgu133a.db?
> Again, sorry if this is obvious, I'm still learning.
>
> Hannah
>
> ________________________________________
> From: Marc Carlson [mcarlson at fhcrc.org]
> Sent: Wednesday, April 22, 2009 2:23 PM
> To: James W. MacDonald
> Cc: Thomas Hampton; Tipney, Hannah; bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Appropriate Probe annotation for HT-HGU133A chips
>
> A nice response as always Jim.  :)
>
> For Thomas and anyone else who might be wondering about this, please do
> not use old annotation packages.  Annotations are always changing as we
> learn more, which is why we update all of them for each release.  Even
> if you don't want to do cool stuff with databases, you will still
> benefit from using annotations that are more current.
>
>
>   Marc
>
>
>
> James W. MacDonald wrote:
>   
>> Hi Tom,
>>
>> Thomas Hampton wrote:
>>     
>>> While we are on this subject, what is the difference between this "db"
>>> and the old way of annotation I still use?
>>>
>>> I use something like:
>>>
>>> librarary(hgu133a2)
>>>
>>> Am I a dinosaur?
>>>       
>> Yes. And you are obviously using a very old version of R/BioC, so you
>> are doubly a dinosaur ;-D
>>
>> The difference for the average dinosaur-like creature is not
>> noticeable. The new annotation packages are based on an underlying
>> SQLite database rather than the old-style environments, but the fine
>> folks in Seattle have written gobs of code that allow you to interact
>> with the database as if it were an environment.
>>
>> For instance,
>>
>> library(hgu133a2.db)
>> get("1007_s_at", hgu133aSYMBOL)
>>
>> will work just as you expect. However, there are lots of other really
>> cool things you can do with these new packages that were akin to
>> pulling teeth (or impossible, depending on the task) with the old
>> environment based packages.
>>
>> For instance, say you have a bunch of GO IDs and you want to know what
>> probesets they correspond to:
>>
>>     
>>> library(hgu95av2.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
>>     
>>> goids <- Rkeys(hgu95av2GO)[1:10]
>>> goids
>>>       
>>  [1] "GO:0000002" "GO:0000003" "GO:0000012" "GO:0000018" "GO:0000019"
>>  [6] "GO:0000022" "GO:0000023" "GO:0000027" "GO:0000028" "GO:0000038"
>>     
>>> mget(goids, revmap(hgu95av2GO))
>>>       
>> $`GO:0000002`
>>        TAS        TAS        IMP
>> "32822_at" "36879_at" "37181_at"
>>
>> $`GO:0000003`
>>          IEP
>> "38950_r_at"
>>
>> $`GO:0000012`
>>           IDA           IDA           IEA
>>      "963_at"  "39639_s_at" "160033_s_at"
>>
>> $`GO:0000018`
>>          TAS          TAS          TAS          TAS
>>    "1370_at"   "36227_at" "40474_r_at"   "40407_at"
>>
>> $`GO:0000019`
>>          TAS          TAS          TAS          IDA          IDA
>>   "32869_at" "32870_g_at"   "39233_at"    "1533_at"   "39941_at"
>>
>> $`GO:0000022`
>>        TAS
>> "37171_at"
>>
>> $`GO:0000023`
>>         IC
>> "31816_at"
>>
>> $`GO:0000027`
>>        IEA
>> "33677_at"
>>
>> $`GO:0000028`
>>        IMP        IMP
>> "32412_at" "32413_at"
>>
>> $`GO:0000038`
>>        IEA        IDA        TAS        IEA
>> "36626_at" "36625_at" "37485_at" "39642_at"
>>
>> There are lots of other cool things you can do - see the AnnotationDbi
>> vignette.
>>
>> Best,
>>
>> Jim
>>
>>
>>
>>     
>>> Thanks!
>>>
>>> Tom
>>> On Apr 22, 2009, at 2:51 PM, James W. MacDonald wrote:
>>>
>>>       
>>>> Hi Hannah,
>>>>
>>>> If I'm not mistaken, you want the hgu133a2.db.
>>>>
>>>> Best,
>>>>
>>>> Jim
>>>>
>>>>
>>>>
>>>> Tipney, Hannah wrote:
>>>>         
>>>>> Please forgive this probably obvious question, but I am working with
>>>>> data from the High Throughput Affymetrix chips for the first time. So
>>>>> simply, for the ht-hgu133a chips should I be using the hgu133a.db,
>>>>> hgu133a2.db or hgu133plus2.db Bioconductor probe annotations in
>>>>> conjunction with hthgu133acdf and hthgu133aprobe? I assume hgu133a.db
>>>>> but it is not entirely clear from the Affymetrix site. Thanks in
>>>>> advance Hannah
>>>>> _______________________________________________ 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
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
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>>>>         
>
>
>