Hi Richelle, As Matthew kindly pointed out -- you're knocking on the wrong dooR ;-)
Your question is really most appropriate to the bioconductor mailing list, whose address you can find here (in the "mailing list" tile -- please see that posting guide, too ;-): http://www.bioconductor.org/help/ Make sure you read through the help you can access for the topTable function by running this in your R session: R> library(limma) R> ?topTable Look at the "Value" section, as that is where the description of your returned object is (look at `genelist` in particlar). Lastly -- it will help if you read through "An Introduction to R" so that you're familiar with basics of R programming (vectors, data.frames, etc. and how to subset and index into them in particular). Good luck with your analysis! -steve On Tue, Jun 28, 2011 at 11:00 AM, Ingezz <[email protected]> wrote: > Hello everybody, > > I just started using R for my microarray analysis, so I am quite new to all > of this. For now I have done preprocessing, normalization, limma and > globaltest KEGG pathway analysis. > > I would like to see how each in gene in a certain pathway contributes the > significance of the pathway. Therefore, I would like to combine the output > of limma analysis and the genes that belong to a certain KEGG pathway. > It is simple to get a list of genes that belong to a pathway in a vector, > but I dont know how to pick only those genes from the limma toplist-file, > with all the belonging statistics and make a new datamatrix from that. I > hope my story is a bit clear, cause I dont know the exact R terminology. > > I have googled this, read many online introductions to R, but I cannot find > it. I hope I havent posted this in the wrong place, but I hope that their is > someone who can help me. Is there a function that is capable of picking only > those elements from a datamatrix that correspond to the elements of a list? > That's basically what the question comes down to. > > Many thanks! > > Regards > Richelle > > -- > View this message in context: > http://r.789695.n4.nabble.com/How-to-get-only-those-values-out-of-a-matrix-that-are-in-a-list-tp3630580p3630580.html > Sent from the datatable-help mailing list archive at Nabble.com. > _______________________________________________ > datatable-help mailing list > [email protected] > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/datatable-help > -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact _______________________________________________ datatable-help mailing list [email protected] https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/datatable-help
