[BioC] How to make a db package for Agilent-015354 Bovine Oligo Microarray (4x44K)?

[Marc Carlson]

Hi Kaj,

That error means that your fileName parameter needs to be passed as a 
string.  If you instead pass bov_9712 as you have below (with no 
quotes), R will think that you mean to pass an object that is called 
bov_9712, (instead of the string "bov_9712") and when it gets to the 
point where it is ready to try and actually read that file name into R, 
it will give you the error below.

Please let me know if you still have questions.


  Marc



On 02/18/2013 11:09 PM, Kaj Chokeshaiusaha wrote:
> 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 at 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.
>>
> 	[[alternative HTML version deleted]]
>
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