Andreas Heider | 26 Feb 10:52 2013
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Re: Have troubles with finding Annotations for Bovine and Rhesus\' platforms

Dear Kaj,
I suggest replacing your eArray output file with the former mentioned
"015354_D_GeneList_20061130.txt" (from
http://www.chem.agilent.com/cag/bsp/gene_lists.asp), because the latter one
is much cleaner!
Then move R into the directory containing "015354_D_GeneList_20061130.txt"
and try the following:

library(AnnotationForge)
source("http://bioconductor.org/biocLite.R")
biocLite("org.Bt.eg.db")
library("bovine.db0")
biocLite("org.Bt.eg.db")
library("org.Bt.eg.db")
setwd("bovine_chip")
bovine <- read.table("015354_D_GeneList_20061130.txt",sep="\t",header=T)
write.table(row.names=FALSE,x=bovine[1:2],sep="\t",file="bovine_shrunk.txt",col.names=FALSE,quote=FALSE)
bovine_filepath <- "bovine_shrunk.txt"
makeDBPackage(    "BOVINECHIP_DB",
                affy=FALSE,
                prefix="bovineAgiTest",
                fileName="bovine_shrunk.txt",
                baseMapType="gbNRef",
                outputDir=tempdir(),
                version="0.1.0",
                manufacturer="Agilent",
                chipName="bovineAgiTest",
                manufacturerUrl="www.agilent.com")
install.packages("bovineAgiTest.db", repos=NULL, type="source")
library(bovineAgiTest.db)
head(toTable(bovineAgiTestGO))
head(toTable(bovineAgiTestGENENAME))
head(toTable(bovineAgiTestSYMBOL))
mget("A_73_111883",bovineAgiTestGENENAME)

Good luck,
Andreas

2013/2/19 Kaj Chokeshaiusaha <kajkajkajkajkaj@...>

> Dear all,
>
> I've tried the script as following..
>
> library(AnnotationForge)
>
> #Please see the attached "A-GEOD-9712.adf.txt #
>
> bov<-read.table("A-GEOD-9712.adf.txt", skip=13, sep = "\t",
> header = FALSE, as.is = TRUE, fill=T)[,c(2,5)]
>
> output="D:/Progect for MOU/Detailed Projects/Cumulus cell/Cow GPL9712"
> makeDBPackage("BOVINECHIP_DB",
> affy=FALSE,
>  prefix="bov",
> fileName=bov,
> baseMapType="gb",
>  outputDir=output,
> version="1.0.0",
> manufacturer = "Agilent Technologies",
>  chipName = "Agilent-015354 Bovine Oligo Microarray")
>
> then R show me..
>
> Error in read.table(file = file, header = header, sep = sep, quote =
> quote,  :
>   'file' must be a character string or connection
>
> I also try using BOVINE_DB in 'makeDBPackage'. It show me no error but
> doesn't give me back any file
>
> Please suggest me,
> Kaj
>

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