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
when it should be set to
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")