Question: Annotating the Human Gene 2.0 ST Array annotate with hugene20sttranscriptcluster.db hugene20sthsentrezg or hugene20stprobeset
1
gravatar for sofia.figueiredo
2.8 years ago by
sofia.figueiredo10 wrote:

Dear Bioconductor community,

I am working with Human Gene 2.0 ST Array. At the annotation process, I have doubts which .db library to use:

- hugene20sttranscriptcluster.db

- hugene20sthsentrezg.db or

- hugene20stprobeset.db?

Can you please indicate what are the differences between these three and in which situations should I use one or the other .db library?

Many thanks in advance

Sofia

---

Ana Sofia Figueiredo

Bioinformatician, University of Heidelberg

 

 

ADD COMMENTlink modified 2.8 years ago by James W. MacDonald49k • written 2.8 years ago by sofia.figueiredo10

you may try the pd.hugene.2.0.st which provide all the annotations for the platform, I found it easier as a non expert. But for the explication, I will suggest you look at the reference manual of each of theses package, it tell exactly what they do.

ADD REPLYlink written 2.8 years ago by giroudpaul40
Answer: Annotating the Human Gene 2.0 ST Array annotate with hugene20sttranscriptcluster
2
gravatar for James W. MacDonald
2.8 years ago by
United States
James W. MacDonald49k wrote:

The hugene20sttranscriptcluster.db package is for when you have summarized the data at the 'core' level, which is by transcript. The hugene20stprobeset.db package is for when you have summarized at the 'probeset' level, which is roughly the exon level. The hugene20sthsentrezg.db package is for when you summarized using the MBNI re-mapped probesets.

In the vast majority of cases you should use the hugene20sttranscriptcluster.db package. Also, while the pd.hugene.2.0.st package does contain annotation data, those data are simply parsed versions of the Affymetrix annotation csv files, and while giroudpaul may find those easier to deal with, I think that is probably a minority opinion.

 

ADD COMMENTlink written 2.8 years ago by James W. MacDonald49k

Many thanks for your clarifications. I normalized my data again, adding the option target="core" to the rma function and did the annotations with hugene20sttranscriptcluster.db.

Everything is working fine :)

Sofia

ADD REPLYlink written 2.8 years ago by sofia.figueiredo10
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