[BioC] Appropriate Probe annotation for HT-HGU133A chips
Hannah.Tipney at ucdenver.edu
Wed Apr 22 22:57:20 CEST 2009
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.
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.
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:
>> 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,
> 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
>  "GO:0000002" "GO:0000003" "GO:0000012" "GO:0000018" "GO:0000019"
>  "GO:0000022" "GO:0000023" "GO:0000027" "GO:0000028" "GO:0000038"
> > mget(goids, revmap(hgu95av2GO))
> TAS TAS IMP
> "32822_at" "36879_at" "37181_at"
> IDA IDA IEA
> "963_at" "39639_s_at" "160033_s_at"
> TAS TAS TAS TAS
> "1370_at" "36227_at" "40474_r_at" "40407_at"
> TAS TAS TAS IDA IDA
> "32869_at" "32870_g_at" "39233_at" "1533_at" "39941_at"
> IMP IMP
> "32412_at" "32413_at"
> 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
>> On Apr 22, 2009, at 2:51 PM, James W. MacDonald wrote:
>>> Hi Hannah,
>>> If I'm not mistaken, you want the hgu133a2.db.
>>> 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
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>>> James W. MacDonald, M.S.
>>> Douglas Lab
>>> University of Michigan
>>> Department of Human Genetics
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