[BioC] Agi4x44PreProcess 1.4.0 question: use of genes.rpt.agi() and Gene Sets

[Francois Pepin]

Hi Massimo,

I don't know about Agi4x44PreProcess, but Limma can do it with avereps.

In the case of Agilent arrays, I would not recommend doing that from the 
start. The probes mapping to the same genes often do not measure the 
same thing, they can map different splice variants and some can be 
pretty far from the 3' end.

So for differential analysis, I would suggest keeping them different. 
For other analyses that assume one probe per gene, such as gene ontology 
analysis, I would recommend an unbiased method to choose a 
representative probe per gene, for example the highest variance probe or 
the one closest to 3' end.

If you search in the archives, you can find more advice as this is a 
common topic.

Francois

Massimo Pinto wrote:
> Greetings all,
> 
> I realised that I was carrying forward, in my analysis, multiple
> measurements for the same gene that had been carried out using
> independent probes. This is a feature of Agilent arrays, as I
> understand. However, while it is clear to me that Agi4x44PreProcess
> offers a function to summarize replicated probes, called
> summarize.probe(), I cannot see a readily available function that
> performs a similar treatment to replicated genes, i.e. Gene Sets, as
> these are called in the Agi4x44 Package.
> 
> The result of calling
> 
>> genes.rpt.agi(dd, "hgug4112a.db", raw.data = TRUE, WRITE.html = TRUE, REPORT = TRUE)
> 
> is an html list of Gene Sets, but these are not summarized to a
> 'virtual' measurement, like summarize.probe() does for replicated
> probes.
> 
> Is there a reason why one would like to carry on multiple probes for a
> given gene throughout his/her subsequent analysis, including linear
> modeling and gene ontology? If not, is there a function that performs
> the median of such repeats?
> 
> Thank you in advance,
> 
> Yours
> Massimo Pinto
> 
> 
>> sessionInfo()
> R version 2.9.1 (2009-06-26)
> i386-apple-darwin8.11.1
> 
> locale:
> C
> 
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets
> methods   base
> 
> other attached packages:
>  [1] affy_1.22.0             gplots_2.7.0            caTools_1.9
>       bitops_1.0-4.1          gdata_2.4.2             gtools_2.5.0-1
>  [7] hgug4112a.db_2.2.11     RSQLite_0.7-1           DBI_0.2-4
>       Agi4x44PreProcess_1.4.0 genefilter_1.24.0       annotate_1.22.0
> [13] AnnotationDbi_1.6.0     limma_2.18.0            Biobase_2.4.1
> 
> loaded via a namespace (and not attached):
> [1] affyio_1.11.3        preprocessCore_1.5.3 splines_2.9.1
> survival_2.35-4      xtable_1.5-5
> 
> Massimo Pinto
> Post Doctoral Research Fellow
> Enrico Fermi Centre and Italian Public Health Research Institute (ISS), Rome
> http://claimid.com/massimopinto
> 
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