No annotated genes found in universe error using goana and kegga
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emy_66 • 0
@emy_66-14405
Last seen 3.8 years ago

 

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, ...) : 

No annotated genes found in universe

I've also tried using it with my own list of de flybase gene IDs and defining my own universe using a vector of flybase IDs but the same error occurs.

"org.Dm.eg.db" is installed.

Help would be much appreciated. Thanks in advance.

 

My sessionInfo below 

> sessionInfo()

R version 3.4.1 (2017-06-30)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: CentOS release 6.9 (Final)

 

Matrix products: default

BLAS: /opt/Modules/R/3.4.1/lib64/R/lib/libRblas.so

LAPACK: /opt/Modules/R/3.4.1/lib64/R/lib/libRlapack.so

 

locale:

 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              

 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    

 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   

 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 

 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

 

attached base packages:

[1] parallel  stats4    stats     graphics  grDevices utils     datasets 

[8] methods   base     

 

other attached packages:

[1] org.Dm.eg.db_3.5.0   GO.db_3.5.0          AnnotationDbi_1.40.0

[4] IRanges_2.12.0       S4Vectors_0.16.0     Biobase_2.36.2      

[7] BiocGenerics_0.24.0  edgeR_3.12.1         limma_3.26.9        

 

loaded via a namespace (and not attached):

 [1] locfit_1.5-9.1  Rcpp_0.12.13    lattice_0.20-35 digest_0.6.12  

 [5] grid_3.4.1      DBI_0.7         RSQLite_2.0     rlang_0.1.2    

 [9] blob_1.1.0      splines_3.4.1   bit64_0.9-7     bit_1.1-12     

[13] compiler_3.4.1  pkgconfig_2.0.1 memoise_1.1.0   tibble_1.3.4   

 

 

 

limma goana gene set enrichment • 3.2k views
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@gordon-smyth
Last seen 1 hour ago
WEHI, Melbourne, Australia

By default, kegga() will look in rownames(lrt) for the gene Ids.

KEGG supports either FlyBase CG Ids or Entrez Gene Ids (see below), so you have to supply one or the other. It doesn't support FlyBase FBgn Ids.

> g <- getGeneKEGGLinks("dme")
> head(g)
        GeneID     PathwayID
1 Dmel_CG10160 path:dme00010
2 Dmel_CG10202 path:dme00010
3 Dmel_CG10467 path:dme00010
4 Dmel_CG10924 path:dme00010
5 Dmel_CG10996 path:dme00010
6 Dmel_CG11140 path:dme00010
> g <- getGeneKEGGLinks("dme",convert=TRUE)
> head(g)
  GeneID     PathwayID
1  45880 path:dme00010
2  36649 path:dme00010
3  38697 path:dme00010
4  37130 path:dme00010
5  32345 path:dme00010
6  45398 path:dme00010

Note that org.Dm.eg.dg is not relevant here as it isn't used in a KEGGA analysis

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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 universe

Also

go.de=goana(lrt,species="Dm")

Error in goana.default(de = DEGenes, universe = universe, ...) : 

No genes found in universe

I've also tried storing the gene ids elsewhere but still cannot get it working. Is there something wrong with specifying flybaseIDs? If I have numeric row names and take out the species='Dm' the program assumes human entrez IDs and I get a result (albeit wrong).

 

 

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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 fly-base IDs are assumed.'

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Yes, I agree that is confusing. I must admit that I am not very familiar with Drosophila and I was not sure what to call the FlyBase CG Ids. I will try to clarify it in the documentation.

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