User: Gilbert Feng

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Gilbert Feng300
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Posts by Gilbert Feng

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Comment: C: GeneAnswer package Query
... Can you run dim(getEnrichmentInfo(xx)) ? Because there is a warning here, "Some specified categories might not be statistical significant! Only show significant categories.". So if there is none significant pathway based on geneAnswersBuilder, you can't get the network. Gilbert From: Reema Singh & ...
written 6.6 years ago by Gilbert Feng300
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Answer: A: GeneAnswer package Query
... Hi, Reema Please give us more info, like Steve and Sean stated in their previous responses. Basically, for geneAnswersConceptNet(), xx should be an instance of GeneAnswers. So you can run > class(xx) If the output is not like this, [1] "GeneAnswers" attr(,"package") [1] "GeneAnswers" You ne ...
written 6.6 years ago by Gilbert Feng300
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total gene number for a given species in reactome.db
... Hello, I am using reactome.db for over-representive enrichment test, so I wonder how I can get the total gene number for a given species in reactome.db. For example, how many human genes (unique Entrez Ids) are annotated in reactome.db? Is there any simple way to get this number besides counting th ...
pathways written 6.7 years ago by Gilbert Feng300 • updated 6.7 years ago by Marc Carlson7.2k
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Answer: A: Which resources for pathway analysis?
... Hi, January GeneAnswers integrates GO, DO, KEGG, and caBIO(NCI, Reactome and Biocarta) as well as gene interaction and entrez keywords search for gene set enrichment analysis. Finally, it can automatically generate a html report for one or multiple groups of gene set enrichment analysis with intera ...
written 8.1 years ago by Gilbert Feng300
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Answer: A: NCI pathways to graphNEL
... Hi, Laurent Basically, GeneAnswers is designed for enrichment test based on different annotation libraries. In your case, if you just want to retrieve one or several NCI pathways, you can use standard xml query to obtain them from caBIO site. Then reconstruct the pathway by yourself (GeneAnswers al ...
written 8.2 years ago by Gilbert Feng300
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Comment: C: Hypergeometric test with Disease Ontology
... Hi, Vincent That's a good question. Currently, DO.obo file contains some synonyms for each DO term/ID. Our collaborators are working on curation right now. I'll talk to them about this. So far, what I can think is to retrieve the synonyms from DO.obo and use some text mining tools to find the DO id ...
written 8.2 years ago by Gilbert Feng300
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Comment: C: Hypergeometric test with Disease Ontology
... Hi, Ted Yes, your codes about mygenepool and mygenes are correct. I didn't clearly state them in my previous email. Sorry about that. myDOLite should be built by DOLite and mygenepool, not mygenes. So currently, myDOLite is a customized annotation library and when you build a geneAnswers instance, ...
written 8.2 years ago by Gilbert Feng300
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Comment: C: Hypergeometric test with Disease Ontology
... Hi, Ted If I correctly understand your question, you have your own gene pool, don't you? In that case, GeneAnswers still can handle that. What you need is to build a customized DOLite list to run analysis. For example, if your genes are mygenes(an unique Entrez GENE ID vector) myDOLite <- lapp ...
written 8.2 years ago by Gilbert Feng300
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Comment: C: Hypergeometric test with Disease Ontology
... Yes, Peter, that's true. The 1st version GeneAnswers has such question, but the current one has solved it. In geneAnswerBuilder, there is new parameter, known(default is TRUE), which means only use annotated genes as the gene pool. There is another parameter,totalGeneNumber, for customized annotatio ...
written 8.2 years ago by Gilbert Feng300
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Comment: C: Hypergeometric test with Disease Ontology
... Thanks, Peter. Yes, Fundo is also a good choice. It also uses hypergeometric test, but it can show the GeneRef evidence for the association between diseases and genes. Gilbert On 1/27/11 9:39 AM, Peter Robinson wrote: > On 01/27/2011 04:17 PM, Gilbert Feng wrote: >> Hi, Ted >> >& ...
written 8.2 years ago by Gilbert Feng300

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