[BioC] Affy Tiling Array & Oligo

[Naira Naouar]

Hello Joseph,

Which array are you using??
First you need to create a CDF for your affymetrix tiling. For that you 
need the makeplatformdesign package.
You also have to take from Affymetrix the BPMAP and CIF files available 
for your tiling array.


***** R Code ****
 > library(makePlatformDesign)
 > makePDpackage("AFFY_TILING.bpmap",file1="AFFY_TILING.cif", 
manufacturer="affymetrix", type="tiling")


Then you check and build the package you obtained (in unix: with "R CMD 
check AFFY_TILINGcdf" and "R CMD build AFFY_TILINGcdf")
The name of the cdf (I put here as example AFFY_TILINGcdf) will be given 
by makePDpackage command.

Then you have a cdf for your tiling :) You can read your cel files with 
oligo package:

 >library(oligo)
 >library(AFFY_TILINGcdf)

data=read.celfiles(list.celfiles(),pk="AFFY_TILINGcdf")

Here you have access to all the data available on the tiling array. 
Then, depending on the analysis you want to do, you will need to map the 
probes on the array to genes or something else...

Regards,
Naira




joseph wrote:
> Hello
> The vignette "An Introduction to the Oligo Package" addresses only Affymetrix SNP Arrays. Does any one have an example of how to analyze Affy tiling arrays with oligo and is willing to share it?
> Thanks
> Joseph Dhahbi
> CHORI
>
>
>
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Naira Naouar 

Tel:+32 (0)9 331 38 63                      
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927, 9052 Gent, BELGIUM
nanao at psb.ugent.be                         http://www.psb.ugent.be