need help with microarray GO enrichment using goana
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mat149 ▴ 80
@mat149-11450
Last seen 9 days ago
United States

Hello,

I am attempting to perform a gene ontology enrichment analysis. I am applying the goana function to my MArrayLM object returned from the eBayes fit. When I use the following code, it returns an error:

 

eset<-rma(CELdat, background=TRUE, normalize=TRUE, subset=NULL, target="core")     
library(affycoretools)
eset <- annotateEset(eset, annotation(eset))


library(org.Dr.eg.db)
fd <- fData(eset)
fd$ENTREZID <- mapIds(org.Dr.eg.db, as.character(fd$SYMBOL), "ENTREZID","SYMBOL",multiVals="first")
fData(eset) <- fd

library(limma)
design = model.matrix(~ 0 + f)
colnames(design)=c("control","morphant","rescue")
design
data.fit = lmFit(eset,design)
contrast.matrix = makeContrasts(morphant-control,rescue-control,morphant-rescue,levels=design)
data.fit.con = contrasts.fit(data.fit,contrast.matrix)
data.fit.eb = eBayes(data.fit.con)

 

go <- goana(data.fit.eb, coef=1,geneid=data.fit.eb$genes$ENTREZID,species="dre",convert=TRUE)

Error in goana.default(de = DEGenes, universe = universe, ...) : 
  org.dre.eg.db package required but not not installed (or can't be loaded)

 


I downloaded the packages (org.Dr.eg.db, pd.zebgene.1.1.st) for the microarray platform (Affy 1.1 ST Zebrafish Gene Array) but it seemingly cant be loaded. Can anyone help me with the GO enrichment here?

Thanks,

Matt

 

R version 3.3.1 (2016-06-21)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] edgeR_3.14.0             limma_3.28.21            org.Dr.eg.db_3.3.0      
 [4] AnnotationDbi_1.34.4     affycoretools_1.44.3     pd.zebgene.1.1.st_3.12.0
 [7] RSQLite_1.0.0            DBI_0.5-1                oligo_1.36.1            
[10] Biostrings_2.40.2        XVector_0.12.1           IRanges_2.6.1           
[13] S4Vectors_0.10.3         Biobase_2.32.0           oligoClasses_1.34.0     
[16] BiocGenerics_0.18.0 

 

goana limma • 2.1k views
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@gordon-smyth
Last seen 4 hours ago
WEHI, Melbourne, Australia

You have typed species="dre" when you meant species="Dr". You have to use exactly the right letters and capitalization.

There is no argument 'convert' for goana() and no need to convert IDs anyway. Please read the help page. I think you may be getting confused with kegga(). The two functions have slightly different arguments because goana() uses annotation information stored in Bioconductor annotation packages whereas kegga() uses annotation read from the KEGG webpage. For example, you have to use Bioconductor-style species names for goana() instead of KEGG-style names.

Also, did you know that you can just use geneid="ENTREZID"? You don't have to specify the whole object path.

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Thank you Gordon, this worked perfectly and the information is very helpful!

I may be wrong but geneid="ENTREZID" unfortunately does not work with the pd.zebgene.1.1.st annotation package. I am not aware of a zebgene11sttranscriptcluster.db comparable to ~ hugene11sttranscriptcluster.db so that was the only way I could find to obtain Entrez ID's.

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The goana() function does not make any use of pd.zebgene.1.1.st. As I say, you can just use geneid="ENTREZID" in the goana() call. A correct call would be:

go <- goana(data.fit.eb, coef=1, geneid="ENTREZID", species="Dr")
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you were correct, thanks again!

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