[BioC] Have troubles with finding Annotations for Bovine and Rhesus\' platforms

[James W. MacDonald]

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