[BioC] R: Is it possible to analyze GOs for lists of genes obtained from a "top-down" approach?

[Manca Marco (PATH)]

Dear Amit,

thank you for your valuable suggestion. I have been using DAVID and Panther for those analyses up to now, but I feel more comfortable using R and Bioconductor and I am sincerely glad something exist which could help me doing what I wanted.

I am downloading and trying it now.

Best regards,
Marco

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Marco Manca, MD
University of Maastricht
Faculty of Health, Medicine and Life Sciences (FHML)
Cardiovascular Research Institute (CARIM)
PO Box 616
6200 MD Maastricht

E-mail: m.manca at path.unimaas.nl
Office telephone: +31(0)433874633
Personal mobile: +31(0)626441205
Twitter: @markomanka
________________________________________
Da: amit mandal [amit491 at gmail.com]
Inviato: lunedì 10 agosto 2009 15.25
A: Manca Marco (PATH)
Cc: bioconductor at stat.math.ethz.ch
Oggetto: Re: [BioC] Is it possible to analyze GOs for lists of genes obtained   from a "top-down" approach?

hello,
  You might be interested in the topGO<http://bioconductor.org/packages/2.4/bioc/html/topGO.html> package from BioC. Here one would need a list of genes with respective p-values to start with. Nevertheless, a object of type topGOdata would have to be created. That more pertinent than needing to create an ExpressionSet. Creating such objects/ classes helps to apply statistical tests for inference.
      Using online GO analysis tools (DAVID<http://david.abcc.ncifcrf.gov/>) can be another option.

regards,


On Mon, Aug 10, 2009 at 5:15 PM, Manca Marco (PATH) <m.manca at path.unimaas.nl<mailto:m.manca at path.unimaas.nl>> wrote:

Dear Bioconductors,

good morning. I hope my email finds you well.

I would like to ask for your help concerning a task that I suppose being quite trivial but through which I am unable to find my way.

Is it possible to get GOIDs for lists of genes obtained from (as instance) webservices or published papers?

Reading annotate and GOstats' vignettes I can only find information about processing lists obtained by microarray analyses and organized as ExpressionSets...

Could you point me to any relevant reading?

Thank you in advance for your suggestions.

My best regards,
Marco



--
Marco Manca, MD
University of Maastricht
Faculty of Health, Medicine and Life Sciences (FHML)
Cardiovascular Research Institute (CARIM)
PO Box 616
6200 MD Maastricht

E-mail: m.manca at path.unimaas.nl<mailto:m.manca at path.unimaas.nl>
Office telephone: +31(0)433874633
Personal mobile: +31(0)626441205
Twitter: @markomanka
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--
amit mandal
Graduate Student
Genomics & Molecular Medicine lab
Institute of Genomics & Integrative Biology (IGIB)
Delhi

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The robbed that smiles, steals something
from the thief.
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