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Nianhua Li
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870
@nianhua-li-1606
Last seen 10.3 years ago
Hi, Morten,
You can build one yourself:
1. Download the annotation xls file from
http://microarray.genome.duke.edu/spotted-arrays/available-arrays
It is under "List of Genes".
2. Save the xls file as csv file (say "anno.csv"), and extract the
oligo_id to
Genbank mapping from it:
anno <- read.csv("anno.csv", header=T, stringsAsFactors=F)
res <- anno[,c(3, 10)]
na_id <- which(res[,1]=="")
res <- res[-na_id, ]
na_acc <- which(res[,2]=="")
res[na_acc, 2] <- "NA"
res <- paste(res[,1], res[,2], sep="\t", collapse="\n")
cat(res, file="operon_human_v3_gb.txt")
3. Create metadata package:
library(AnnBuilder)
operon <- function(pkgPath, version) {
ABPkgBuilder(baseName="operon_human_v3_gb.txt",
baseMapType="gb",
pkgName="OperonHumanV3",
pkgPath=pkgPath,
organism="Homo sapiens",
version=version,
author=list(
authors="YourName",
maintainer="YourName <youremail at="" email.com="">"
)
)
}
operon(getwd(), "1.1.0")
Make sure your GO is up-to-date. You can use "biocLite" to get it.
I just built one. If you can't create it yourself, I can at least
email it to
you. But it will be better to build it yourself so that you can
modify/update it
as you want. Good luck!
nianhua