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

Massimo Pinto pintarello at gmail.com
Tue Oct 20 12:06:06 CEST 2009

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

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,

Massimo Pinto

> sessionInfo()
R version 2.9.1 (2009-06-26)


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

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