User: Adrian Alexa

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Adrian Alexa400
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Posts by Adrian Alexa

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Comment: C: TopGo package
... Hi Qian, the problem is in the following line of code: > goID <- allResD7inf[1,"GO:0050878"] The result will be that 'goID == NULL' and therefore you get the error when calling the 'printGenes()'. The 'GenTable()' function returns a data.frame, so 'allResD7inf[1, ]' will be a data.frame wit ...
written 5.2 years ago by Adrian Alexa400
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Student Internships at Illumina Cambridge Ltd, UK
... Dear all, The Computational Biology group at Illumina Cambridge Ltd, UK, is offering several projects for student internships. The topics of the project are: - BaseSpaceR - a package for developing NGS analysis methods on Illumina's BaseSpace platform. - Metrics analytical framework for g ...
sequencing basespacer written 5.3 years ago by Adrian Alexa400
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Comment: C: Find enriched GO terms, given a list of GO terms of interest and background GO t
... Hi JJ, yes, you should be able to do that with topGO. Please read through Section 4.3 in the package vignette on how to use custom annotations: http://www.bioconductor.org/packages/release/bioc/vignettes/topGO/inst /doc/topGO.pdf You can't specify a level and chose to test only the GO terms on tha ...
written 5.4 years ago by Adrian Alexa400
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New GO terms after TopGO enrichment? (updated)
... Hi Bernardo, this is normal and it is a consequence of the True Path Rule. After all, you want to perform the enrichment test on the GO ontology not only on a selected number of GO terms. Regards, Adrian On Tue, Oct 29, 2013 at 7:20 PM, Bernardo Bello wrote: > Possible answer -> These ...
go topgo written 5.6 years ago by Adrian Alexa400 • updated 5.6 years ago by biotech160
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topGO analysis returns different gene counts for category than given for non-model organism
... Hi Diana, the 'issue' you are seeing is due to the "True Path Rule". I suspect that the geneID2GO mappings gives only the specific annotation to a particular GO term. However during the mapping of the genes to the GO hierarchy the genes annotated to a GO term are pushed up the hierarchy. So a GO t ...
annotation go topgo written 5.8 years ago by Adrian Alexa400 • updated 5.8 years ago by Diana Toups Dugas20
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Answer: A: [topGO] More flexible way to select 'interesting' genes
... Hi Enrico, unfortunately, the simple answer is NO. There is not facility to have the geneSelectionFun filter on anything but the gene scores. It is a bit of an old design with limitations, sorry for that. You might be able to hack a solution, but it can get messy. There are two methods that use th ...
written 5.9 years ago by Adrian Alexa400
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Answer: A: topGO Fisher test error
... Hi Bruno, there are a couple of issues with your code. First, the problem stands in the way 'probbe2GO' is formatted. It should be a named list, where the names are the probe ID and a list entry is a character string of GO IDs (the ones to which a probe ID is annotated). However, your 'probe2GO' o ...
written 6.2 years ago by Adrian Alexa400
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Answer: A: Student Internships at Illumina Cambridge Ltd.
... Dear all, The Computational Biology group at Illumina Cambridge Ltd, UK, is offering six projects for student internships. The topics of the project are: - Interactive visualisation of genomic information - R API for mining and visualizing metric data objects - Learning models for predic ...
written 6.3 years ago by Adrian Alexa400
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Student Internships at Illumina Cambridge Ltd.
... Dear all, The Computational Biology group at Illumina Cambridge Ltd, UK, is offering six projects for student internships. The topics of the project are: - Interactive visualisation of genomic information - R API for mining and visualizing metric data objects - Learning models for predic ...
sequencing written 6.3 years ago by Adrian Alexa400
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how to supply a vector/list of results to GenTable in topGO?
... Hi Aaron, The "R magic" is to use do.call() function. Check the manual for more details on its functionality. The only 'trick' here is to build the second argument. > data(GOdata) > data(results.tGO) > ls() [1] "GOdata" "resultFisher" "resultKS" > res <- list(fisher = result ...
go process topgo written 6.4 years ago by Adrian Alexa400

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Popular Question 5.2 years ago, created a question with more than 1,000 views. For topGO enrichment using ensembl gene list

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