Gene Ontology link in aaf.handler() not working
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Entering edit mode
bjwiley23 • 0
@bjwiley23-20637
Last seen 3.4 years ago

Hi,

I am working through the Bioconductor Test Cases by Hahne, Huber, Gentleman, & Falcon (I know they are 10 years old but still relevant) and when creating the annotation table with aafTableAnn the links in the second to last column of aaf.handler() for Gene Ontology are incorrect. I believe the prefix is just wrong. Instead of for example accession GO:0070588 the link from the aaf.hander is set to

http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&query=GO:0070588

when it should be set to

http://amigo.geneontology.org/amigo/term/GO:0070588

Has anyone else noticed this?

library(CLL)
library(annaffy)
library(annotate)

data("CLLbatch")
sampleNames(CLLbatch)
data("disease", package = "CLL")
rownames(disease) <- disease$SampleID
sampleNames(CLLbatch) <- sub("\\.CEL$", "", sampleNames(CLLbatch))
mt <- match(rownames(disease), sampleNames(CLLbatch))
vmd <- data.frame(labelDescription = c("Sample ID",
                                      "Disease status: progressive or stable disease"))
phenoData(CLLbatch) <- new("AnnotatedDataFrame", data = disease[mt,], varMetadata = vmd)
CLLbatch <- CLLbatch[, !is.na(CLLbatch$Disease)]
badArray <- match("CLL1", sampleNames(CLLbatch))
CLLB <- CLLbatch[, -badArray]
CLLrma <- rma(CLLB)
CLLf <- nsFilter(CLLrma, remove.dupEntrez = F, var.cutoff = .5)$eset

table_ <- topTable(CLLeb, coef = 2, adjust.method = "BH", n=10)
genenames <- as.character(row.names(table_))
atab <- aafTableAnn(genenames, "hgu95av2.db", aaf.handler())
saveHTML(atab, file="GeneList2.html")

browseURL("GeneList2.html")
annaffy aafTableAnn Gene Ontology aaf.handler() • 666 views
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3
Entering edit mode
@james-w-macdonald-5106
Last seen 3 hours ago
United States

Fixed in devel:

> example(aafGO)

aafGO> if (require(hgu95av2.db)) {
aafGO+     data(aafExpr)
aafGO+     probes <- featureNames(aafExpr)
aafGO+     gos <- aafGO(probes, "hgu95av2.db")
aafGO+     show(gos[6:10])
aafGO+ }
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db
<snip>
> getURL(gos[[1]][[1]])
[1] "http://amigo.geneontology.org/amigo/term/GO:0001501"
> sessionInfo()
R Under development (unstable) (2019-03-19 r76252)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

Matrix products: default
BLAS:   /data/oldR/R-devel/lib64/R/lib/libRblas.so
LAPACK: /data/oldR/R-devel/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] hgu95av2.db_3.2.3    org.Hs.eg.db_3.8.0   annaffy_1.55.1      
 [4] KEGG.db_3.2.3        GO.db_3.7.0          AnnotationDbi_1.45.1
 [7] IRanges_2.17.4       S4Vectors_0.21.21    Biobase_2.43.1      
[10] BiocGenerics_0.29.2 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1      digest_0.6.18   DBI_1.0.0       RSQLite_2.1.1  
 [5] blob_1.1.1      tools_3.6.0     bit64_0.9-7     bit_1.1-14     
 [9] compiler_3.6.0  pkgconfig_2.0.2 memoise_1.1.0  
> 

Since we are going to release the new version on 3 May, there's no real reason to push to the (soon to be old) release version.

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