Dear all, I’m working with Agilent 4X44K microarrays (annotation db hgug4112a.db) and a genelist with differentially expressed genes with Agilent Ids. I would like to try topGO for GO analysis. I have read the vignette but find it difficult to translate the code to fit my purpose. How should the code mentioned below be adapted: > sampleGOdata <- new("topGOdata", description = "Simple session", ontology = "BP",allGenes = geneList, geneSel = topDiffGenes, nodeSize = 10, annot = annFUN.db, affyLib = affyLib) Any example on topGO using other examples would be helpful. Thank you for your support, Patrick De Boever Patrick De Boever, PhD, MSc Flemish Institute for Technological Research (VITO) Unit Environmental Risk and Health, Toxicology group Industriezone Vlasmeer 7, 2400 Mol, Belgium Tel. + 32 14 33 51 45 Fax. + 32 14 58 05 23 patrick.deboever@vito.be<mailto:patrick.deboever@vito.be> Visit our website: www.vito.be/english<http: www.vito.be="" english=""> --- This e-mail, any attachments and the information it contains are confidential and meant only for the use of the addressee(s) only. Access to this e-mail by anyone other than the addressee(s) is unauthorized. If you are not the intended addressee (or responsible for delivery of the message to such person), you may not use, copy, distribute or deliver to anyone this message (or any part of its contents) or take any action in reliance on it. In such case, you should destroy this message and notify the sender immediately. If you have received this e-mail in error, please notify us immediately by e-mail or telephone and delete the e-mail from any computer. All reasonable precautions have been taken to ensure no viruses are present in this e-mail and its attachments. As our company cannot accept responsibility for any loss or damage arising from the use of this e-mail or attachments we recommend that you subject these to your virus checking procedures prior to use. [[alternative HTML version deleted]]

Hi Patrick, On 9/12/2010 3:04 PM, De Boever Patrick wrote: > Dear all, > > I?m working with Agilent 4X44K microarrays (annotation db > hgug4112a.db) and a genelist with differentially expressed genes with > Agilent Ids. I would like to try topGO for GO analysis. I have read > the vignette but find it difficult to translate the code to fit my > purpose. How should the code mentioned below be adapted: >> sampleGOdata<- new("topGOdata", description = "Simple session", >> ontology = "BP",allGenes = geneList, geneSel = topDiffGenes, >> nodeSize = 10, annot = annFUN.db, affyLib = affyLib) > > Any example on topGO using other examples would be helpful. I see you are working through the topGO vignette. As part of that effort, it might be worth it to look at the objects are being used as part of the vignette, so you might be able to create something similar using your data. For instance: > head(geneList) 1095_s_at 1130_at 1196_at 1329_s_at 1340_s_at 1342_g_at 1.0000000 1.0000000 0.6223795 0.5412240 1.0000000 1.0000000 Which in the text is described as the probeset IDs and p-values for 323 of the probesets on the hgu95av2 chip. Now I suppose you have some data and corresponding p-values, so I leave it up to you to create a similar named vector, using your data. The only other thing that will be different is the argument for affyLib. Just two code chunks prior to the one you note in your email, you can see where the affyLib comes from. It might be a bit obscure what that is exactly, but you _could_ install the ALL package yourself, submit that code, and see for your self what the affyLib object is. But to save you that effort, as the ALL package is a bit large, it is simply the name of the annotation package. So you could just use affyLib = "hgug4112a.db". Best, Jim > > Thank you for your support, > > Patrick De Boever > > > Patrick De Boever, PhD, MSc Flemish Institute for Technological > Research (VITO) Unit Environmental Risk and Health, Toxicology group > Industriezone Vlasmeer 7, 2400 Mol, Belgium Tel. + 32 14 33 51 45 > Fax. + 32 14 58 05 23 > patrick.deboever at vito.be<mailto:patrick.deboever at="" vito.be=""> > > Visit our website: www.vito.be/english<http: www.vito.be="" english=""> > > > --- This e-mail, any attachments and the information it contains are > confidential and meant only for the use of the addressee(s) only. > Access to this e-mail by anyone other than the addressee(s) is > unauthorized. If you are not the intended addressee (or responsible > for delivery of the message to such person), you may not use, copy, > distribute or deliver to anyone this message (or any part of its > contents) or take any action in reliance on it. In such case, you > should destroy this message and notify the sender immediately. If > you have received this e-mail in error, please notify us immediately > by e-mail or telephone and delete the e-mail from any computer. All > reasonable precautions have been taken to ensure no viruses are > present in this e-mail and its attachments. As our company cannot > accept responsibility for any loss or damage arising from the use of > this e-mail or attachments we recommend that you subject these to > your virus checking procedures prior to use. > > > > [[alternative HTML version deleted]] > > > > > _______________________________________________ Bioconductor mailing > list Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues