[BioC] Can my problem be addressed with Bioconductor?

Michela Leonardi [guest] guest at bioconductor.org
Tue Jun 17 20:14:08 CEST 2014

Dear All,
I am very new to Bioconductor and to Gene Ontology analyses, so please forgive me if my question is trivial.
I have as "universe" a list of SNPs (not all of them) from the Affymetrix 6.0 SNPchip. After some population genetics analyses I defined a subset of particular interest to me (i.e. showing signal of selection). I would like to  analyze the subset of SNPs (or, better, associated genes) in order to test for gene enrichment for gene ontology categories.

My first question is: are GOstats and topGO the right tools to perform this analysis on the kind of data I have (lists of genes as text files)?

And if yes... I started "playing around" with Bioconductor and I got stuck with the association: I could not find the way to tell to the program that I used the Affymetrix 6.0 SNPchip. Could you point me towards some link or document helping me going through all passages needed to do the analyses I need?

Thanks a lot for you help

Michela Leonardi

 -- output of sessionInfo(): 

R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

[1] it_IT.UTF-8/it_IT.UTF-8/it_IT.UTF-8/C/it_IT.UTF-8/it_IT.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] tools_3.1.0

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