User: artur

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artur70
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Posts by artur

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Comment: C: Select the annotation level during GO enrichment
... Thanks for your answer, This is a really good idea when working with GOstats. However, this apporach will work quite good if the GO IDs enriched are not that many. In case of 50-70 GO IDs, this would require quite a lot of manual work. I'm just wondering if there is a way/package to subset the enric ...
written 3.1 years ago by artur70
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Select the annotation level during GO enrichment
... I am working with a non model organism and I performed a gene set enrichment test using topGO and GOstats. The analysis in both cases worked properly, but I would need an enrichment for a higher level of GO (less specific). Is someone aware of a way to select the annotation level to use for performi ...
go gostats topgo written 3.2 years ago by artur70 • updated 3.2 years ago by James W. MacDonald45k
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Comment: C: AnnotationForge: org.Xx.eg.db created with makeOrgPackage() is missing org.Xx.eg
... Thank you very much for your answer Marc.. It would be great if this update will be performed. Thanks again. ...
written 3.2 years ago by artur70
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AnnotationForge: org.Xx.eg.db created with makeOrgPackage() is missing org.Xx.egGO object.
... In the light of previous question I explain here in more detail my problems with the creation of an organism package. I tried to create my orgnaism package using the function makeOrgPackage() of the AnnotationForge package.These are my original data.frames ​ ​> head(genes.goID) GID ...
organismdb annotationdbi annotationforge written 3.2 years ago by artur70 • updated 3.2 years ago by Marc Carlson7.2k
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Comment: C: Create object "Go3AnnDbBimap" and include it in a org.Xx.eg.db package to use wi
... Thank you very much Laurent. I think I will follow your suggestion. ...
written 3.2 years ago by artur70
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Comment: C: Error with goProfiles and goTools: "object org.XX.egGO not found"
... Sorry about that, I will avoid it in the future! ...
written 3.2 years ago by artur70
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Comment: C: Error with goProfiles and goTools: "object org.XX.egGO not found"
... Hi Laurent, thank you for your answer. As you can see in the org.Hs.eg.db  > ls("package:org.Hs.eg.db") [1] "org.Hs.eg" "org.Hs.eg.db" "org.Hs.eg_dbconn" "org.Hs.eg_dbfile" "org.Hs.eg_dbInfo" "org.Hs.eg_dbschema" [7] "org.Hs.egACCNUM" ...
written 3.2 years ago by artur70
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Comment: C: Error with goProfiles and goTools: "object org.XX.egGO not found"
... I understood that i have to create my org.Xx.egGO map, which should be an object of class "Go3AnDbBimap". Looking into > colnames(org.Hs.egGO) [1] "gene_id" "go_id" "Evidence" "Ontology" I see that I have all these information already in my package keytypes(org.Psp.FOBEG1.eg.db) ​[1] " ...
written 3.2 years ago by artur70
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Create object "Go3AnnDbBimap" and include it in a org.Xx.eg.db package to use with goProfiles and goTools
... I would like to compare the GO enrichments of several gene clusters. I tried to use goProfles and goTools. Since I am using a non model organism I build my own organism package using AnnotationForge > keytypes(org.Psp.FOBEG1.eg.db) [1] "Locus"        "EnsemblNames" "GID"          "GO"       ...
go goprofiles annotationforge bimap written 3.2 years ago by artur70
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error: "'names' attribute [16] must be the same length as the vector [2]", using Making Organism packages use of makeOrgPackage()
... I am creating my annotation package using makeOrgPackage(). I followed the instruction here: http://www.bioconductor.org/packages/release/bioc/vignettes/Annotation Forge/inst/doc/MakingNewOrganismPackages.htm This are the dataframes and the commands I used: > test3 GID Gene Name Protein Name ...
annotation go annotationforge written 3.2 years ago by artur70 • updated 3.2 years ago by Marc Carlson7.2k

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