Question: Gene Ontology link in aaf.handler() not working
0
gravatar for bjwiley23
5 months ago by
bjwiley230
bjwiley230 wrote:

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")
ADD COMMENTlink modified 5 months ago by James W. MacDonald51k • written 5 months ago by bjwiley230
Answer: Gene Ontology link in aaf.handler() not working
3
gravatar for James W. MacDonald
5 months ago by
United States
James W. MacDonald51k wrote:

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.

ADD COMMENTlink written 5 months ago by James W. MacDonald51k
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