[BioC] differences among pd.mogene.1.0.st.v1, mogene10sttranscriptcluster.db and mogene10stprobeset.db

James W. MacDonald jmacdon at uw.edu
Thu Sep 27 15:55:15 CEST 2012

Hi Javier,

On 9/27/2012 7:36 AM, Javier Pérez Florido wrote:
> Dear list,
> What are the differences between these two packages 
> (mogene10sttranscriptcluster.db and mogene10stprobeset.db)?
> As far as I know, the first annotation package is used when ST arrays 
> are normalized at the "core" level and the second one when data is 
> normalized at the "probeset" level. Is that right?

If by core and probeset you are referring to arguments for rma() in 
oligo, then yes. Although to be pedantic I should correct you and say 
that you should replace normalize with summarize. Regardless of the 
summarization level, all data are normalized at the probe level. It is 
only at the summarization step that there are differences between the 
core and probeset arguments to rma().

In addition, a more satisfying description IMO is transcript and 
probeset, where probeset is roughly equivalent to exon (although some 
probesets span multiple exons).

> Another question is related to the pd.mogene.1.0.st.v1 package, which 
> is the annotation package used in conjunction with the oligo package. 
> What are the differences between this package and the others 
> (mogene10sttranscriptcluster.db and mogene10stprobeset.db)?

Benilton has already answered this question. I would only add that the 
mogene* packages are equivalent to the 'regular' annotation packages 
that exist for the 3'-biased arrays, which map the Affy IDs to various 
other annotation sources, whereas the pd.mogene package is primarily 
intended for internal use by oligo (although I find it quite useful for 
doing things like removing the control probesets which have an annoying 
propensity for appearing in the list of differentially expressed genes).



> Thanks,
> Javier
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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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