User: emy_66

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emy_660
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Posts by emy_66

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Comment: C: No annotated genes found in universe error using goana and kegga
... Oh I see ... in the documentation it is a little confusing since I assumed that fly-base IDs mean FlyBase IDs  'The default for kegga with species="Dm" changed from convert=TRUE to convert=FALSE in limma 3.27.8. Users wanting to use Entrez Gene IDs for Drosophila should set convert=TRUE, otherwise ...
written 12 months ago by emy_660
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Comment: C: No annotated genes found in universe error using goana and kegga
... Thanks for your reply Gordon, Yes, the gene IDs are stored in rowans(lrt) : str(rownames(lrt)) chr [1:1946] "FBgn0000014" "FBgn0000015" "FBgn0000024" "FBgn0000036" ... kegga.de=kegga(lrt,species="Dm") Error in kegga.default(de = DEGenes, universe = universe, ...) :  No annotated genes found in ...
written 12 months ago by emy_660
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No annotated genes found in universe error using goana and kegga
...   Hi, I'm trying to run enrichment analysis on flybase gene ids using goana and kegga from limma. However I keep getting the same error  fit <- glmFit(x, design) lrt <- glmLRT(fit,coef=2) kegga.de=kegga(lrt,species='Dm') Error in kegga.default(de = DEGenes, universe = universe, ...) :  ...
limma goana gene set enrichment written 12 months ago by emy_660

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