[BioC] Human 50k Xba1 Affymetrix arrays cdf file

[Benilton Carvalho]

Hi Christophe,

Note that using makePDpackage under Windows, you must have the tools  
for building R Packages under your OS.

http://www.murdoch-sutherland.com/Rtools/

The link above describe how to set up your system for this.

To build the PDEnv for the XBA array you need the following files:

Mapping50K_Xba240.CDF
Mapping50K_Xba240_probe_fasta
Mapping50K_Xba240_annot.csv

Once you have these files in one directory, start R and change the  
working directory to the one where the files are (you can do this via  
menu/file/change directory or using the command setwd() ).

Then you can use the command:

makePDpackage("Mapping50K_Xba240.CDF",  
"Mapping50K_Xba240_probe_fasta", "Mapping50K_Xba240_annot.csv",  
type="SNP")

to create the package...

Now that the package is create you should build and install it.

Let me know if you need any further help.

b

ps: The following page may be helpful:

http://www.biostat.jhsph.edu/~kbroman/Rintro/Rwinpack.html

On Nov 3, 2006, at 10:19 AM, Christophe Poulet wrote:

> Thanks for your answer,
> I've download and install the "oligo" and "makePDpackage", and the  
> Zipfiles from Affymetrix with success, but R send another error,  
> like this:
> > makePDpackage()
> affymetrix expression
> Error in basename(filein) : argument "designFile" is missing, with  
> no default
>
> I tried to find what and where was the design file but I failed to  
> find it.
>
> I forget to tell you that I am a Biologist who try to work on  
> windows with RGui 2.4.0,  it might be important, because I haven't  
> got Computer Knowledge. You can find a word doc which contains what  
> I have done on R.
>
> Could you tell me what to do, because I don't find this problem in  
> the R FAQs for windows.
> Thanks for your time.
> Best regards.
>
> Christophe Poulet
> Laboratoire de Cytogénétique, CHU
> Université de Liège, Sart Tilman
> christophe.poulet at hotmail.com
>
>
> Lancez des recherches en toute sécurité depuis n'importe quelle  
> page Web. Téléchargez GRATUITEMENT Windows Live Toolbar  
> aujourd'hui ! Essayez-le maintenant !
> <R.doc>