[BioC] build.mappings() from Agi4x44PreProcess is not helping me today

Massimo Pinto pintarello at gmail.com
Fri Jul 17 13:16:39 CEST 2009

Greetings all,

I have re-written my targets file recenty, in the context of an
experiment whose gene expression was measured using Agilent single
color arrays.
Therefore, I ended up having to reload the files specified as my
targets, carry out pre-processing again, run Limma etc.

Preprocessing, however, is now giving my some headaches. _Apparently_,
I have done nothing new compared to what I was doing just about 30
days ago. However, this is what I am getting now:

> mappings=build.mappings(esetPROC,"hgug4112a.db")
Loading required package: GO.db

	The mapping process takes a while ...

Error in function (classes, fdef, mtable)  :
  unable to find an inherited method for function "Ontology", for
signature "character"

> class(esetPROC)
[1] "ExpressionSet"
[1] "Biobase"

Here is a snapshot of my R installation

> 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] GO.db_2.2.11            gplots_2.7.0            caTools_1.9
      bitops_1.0-4.1          gdata_2.4.2
 [6] gtools_2.5.0-1          hgug4112a.db_2.2.5      RSQLite_0.7-1
      DBI_0.2-4               Agi4x44PreProcess_1.4.0
[11] genefilter_1.24.0       annotate_1.22.0
AnnotationDbi_1.6.0     affy_1.22.0             Biobase_2.4.1
[16] limma_2.18.0

loaded via a namespace (and not attached):
[1] affyio_1.11.3        preprocessCore_1.5.3 splines_2.9.1
survival_2.35-4      tools_2.9.1          xtable_1.5-5

I am running the latest version of Agi4x44PreProcess which I installed
today, just in case, via the Mac GUI, with dependencies.

HTH to clarify what my problem is.
Thank you,

Massimo Pinto
Post Doctoral Research Fellow
Enrico Fermi Centre and Italian Public Health Research Institute (ISS), Rome

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