Dear all,

I've tried the script as following..

library(AnnotationForge)

bov_9712<-read.table("A-GEOD-9712.adf.txt", skip=13, sep = "\t",
header = FALSE, as.is = TRUE, fill=T)[,c(2,5)]

#Here at this step bov_9712 contained with 2 column data : Spot_ID and
Genebank#

output="D:/Progect for MOU/Detailed Projects/Cumulus cell/Cow GPL9712"

makeDBPackage("BOVINECHIP_DB",
affy=FALSE,
prefix="bov",
fileName=bov_9712,
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

On Sun, Feb 17, 2013 at 7:07 PM, Kaj Chokeshaiusaha [guest] <
guest@bioconductor.org> wrote:

>
> Dear whom it may concern,
>
> I try to find out the way to make a db package for Agilent-015354 Bovine
> Oligo Microarray (4x44K). Since I'm very new to Bioinformatics and R, would
> you please prove/guide me step by step?
> These are what I plan to do.
>
> 1. I plan to make a table with two column containing with ProbeID and
> Target GeneID with no header.
> 2. I make a db package with makeDBPackage function as indicated in
> "Creating a New Annotation Package using
> SQLForge". I plan to write script exactly the same but have no idea which
> dbschemas to use; BOVINE_DB or BOVINECHIP_DB.
>
> Please help me prove these steps.
> Best Regards,
> Kaj
>
>
>  -- output of sessionInfo():
>
> sessionInfo()
>
> --
> Sent via the guest posting facility at bioconductor.org.
>

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