[BioC] Using ReadAffy with custom CDFs on tiling array data

Arkady bamboowarrior at gmail.com
Wed Jul 23 00:36:49 CEST 2008

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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