Hi John,


	Thanks a lot for your interest in our custom CDF. I think I can answer some of your questions.


	The place you download the tiling array custom CDF has a mapping between original cdf name, and custom CDF name.


	For example, at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/11.0.0/entrezg.asp, there is a line,
Homo sapiens 	TilingHuman10R01 	3104980 	TilingHuman10R01_Hs_ENTREZG
	That means tiling chip number 1 is mapped to custom CDF TilingHuman10R01_Hs_ENTREZG.

	
	So for the tiling arrays celfiles you have, I think you can categorize them by chip number first, then for each chip number, you only need to do ReadAffy and analysis once. 


	Tiling array custom CDF probe package has nothing different than other normal chip probe package. It just included the sequence information for each probe. Some analysis needs this package. But gcrma wouldn't work on tiling array, because tiling array doesn't have mm probe, which is also needed by gcrma.


	We started our custom CDF for tiling array since version 10. We are not sure about its quality, because it has very low probe utilization due to its design. So we decided not to release to biconductor yet.


   	I am still working on version 11, only entrezg is available now. I will discuss with Bioconductor about tiling array custom CDF after all custom CDF type are ready.




Best,
Manhong Dai
 
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
A couple of questions herein.

Background: I'm trying to load the CEL files for the Affy whole-genome
tiling arrays. I have lots and lots of bzipped2 CEL files (3452 of
them). They seem to ask for Wgc_Universal_fe1 as the cdf, and this
package does not appear to be available through Bioconductor,
according to getCDF(cleancdfname("Wgc_Universal_fe1")).

According to some papers I've found, newer custom CDFs are better. So
I tried using some from UMich, but again, they don't appear to be
available in the repository (at least for human tiling 1.0R and 2.0R).

Finally, I downloaded all of the probe and CDF data from UMich and
installed it manually, both the probe and cdf packages. That appeared
to work, and I can load a single CEL file.

Unfortunately, this has left me with several questions.

1. The CEL files contain the names of the original CDFs. How do I
translate those to the names of the custom CDFs? Is there some way to
establish a mapping?

2. How do I deal with multiple CDFs for a single experiment? Do I load
each of my 3452 files separately, specifying the CDF each time?

3. What about the probe packages? Is there a unified package that
contains both pieces (CDF and probes) of information?

4. Why aren't the CDFs for the human tiling arrays made available
through Bioconductor?

Thanks again.
John Woods

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