User: emy_66
emy_66 • 0
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... 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 19 months ago by
emy_66 • 0
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... 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 19 months ago by
emy_66 • 0
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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, ...) :
...
written 19 months ago by
emy_66 • 0
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