Dear Andreas,

I can have a package now!!! Great thanks, I'm very in dept to you and
everyone helping me. I promise to learn my best. Please enlight me a little
bit more. I do want to learn from you.

   1. In the code, 'biocLite("org.Bt.eg.db")' is used two times - before
   and after ' library("bovine.db0"). Why it needs repetition?
   2. My next step is to move on making .db for Rhesus monkey chip. After
   searching for (schemes) using 'available.dbschemas()' function, I can't
   find anything like  'RHESUSCHIP_DB nor 'MONKEYCHIP_DB'. However I
   find 'HUMANCROSSCHIP_DB'. I'm wondering if this is supposed to be used for
   making Rhesus monkey chip?

Thank you very much again for your help.
Best regards,
Kaj


On Tue, Feb 26, 2013 at 4:52 PM, Andreas Heider
<aheider@trm.uni-leipzig.de>wrote:

> 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@gmail.com>
>
>> 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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