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")