[BioC] Appropriate Probe annotation for HT-HGU133A chips

[James W. MacDonald]

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
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: 
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> 

-- 
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