[BioC] Appropriate Probe annotation for HT-HGU133A chips
Tipney, Hannah
Hannah.Tipney at ucdenver.edu
Thu Apr 23 04:59:12 CEST 2009
Jim
Thank you so much for taking the time to explain this - it makes much more sense now :-)
Thanks again.
Hannah
________________________________________
From: James MacDonald [jmacdon at med.umich.edu]
Sent: Wednesday, April 22, 2009 8:34 PM
To: mcarlson at fhcrc.org; Tipney, Hannah
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Appropriate Probe annotation for HT-HGU133A chips
Hi Hannah,
The reason has to do with how Affy named these chips. Back in the day they had a chip called the HG-U133A (and B) that together were supposed to interrogate most of the known human gene transcripts. They then were able to reduce the feature size so that they could get all the content from the A and B chips on a single chip, plus about 5000 more genes. They called this the HG-U133_Plus2 chip. They also had an A chip called the HG-U133A_version2 that was smaller and cheaper - it had pretty much the same content (+/-) as the HG-U133A but used the smaller feature size.
When Affy came out with the HT chips, the first human one had these HG-U133_version2 chips on them. Given the maddeningly inconsistent way Affy names things, they called these the HT-HG-U133A instead of A_version2.
So since the chips are version 2, you should use the version 2 annotation.
Best,
Jim
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
>>> "Tipney, Hannah" <Hannah.Tipney at ucdenver.edu> 04/22/09 5:07 PM >>>
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
>>> 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
>>
>
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