Dear Jim,

Following your advice, my R do calculate something!! These are the script.

library(AnnotationForge)

setwd("D:/Progect for MOU/Detailed Projects/Cumulus cell/Cow GPL9712")

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

write.table(bov_9712, file = "bov_9712.txt", sep = "\t",
     row.names=F, col.names=F)
output="D:/Progect for MOU/Detailed Projects/Cumulus cell/Cow GPL9712"
makeDBPackage("BOVINECHIP_DB",
affy=FALSE,
prefix="bov",
fileName="bov_9712.txt",
baseMapType="gb",
outputDir=output,
version="1.0.0",
manufacturer = "Agilent Technologies",
chipName = "Agilent-015354 Bovine Oligo Microarray")

However, R gives me Error message in the end.

baseMapType is gb or gbNRef
Prepending Metadata
Creating Genes table
Error in sqliteExecStatement(con, statement, bind.data) :
  RS-DBI driver: (RS_SQLite_exec: could not execute1: genes.gene_id may not
be NULL)

Would you please advise me what happens and should I do next?

Best Regards,
Kaj

On Tue, Feb 19, 2013 at 9:16 PM, James W. MacDonald <jmacdon@uw.edu> wrote:

> Hi Kaj,
>
>
> On 2/19/2013 1:51 AM, Kaj Chokeshaiusaha wrote:
>
>> 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 <http://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
>>
>
> Note that the help page has this to say about the fileName argument:
>
> fileName: The path and filename for the file to be parsed.  This can
>           either be an affy csv file or it can be a more classic file
>           type.
>
> In other words, you are supposed to be telling the function where the file
> is. Instead, you read the file in and then tried to pass the data.frame
> object containing those data to the function.
>
> Best,
>
> Jim
>
>
>
>
>
>> 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
>>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>

	[[alternative HTML version deleted]]

