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

[James MacDonald]

Arkady wrote:
> 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?

See ?ReadAffy, specifically the cdfname argument (you _did_ already read 
the help, no?).

> 
> 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?

Again, see ReadAffy(). And good luck reading in 3452 celfiles unless you 
have more RAM than the NSA (or Google - not that there is much 
difference ;-D)

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

See the oligo and pdInfoBuilder packages, which is what you should be 
using for tiling arrays anyway (or the affyTiling package).

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

Mainly because the demand is so low, and there isn't a really easy way 
to analyze them at this time. The barrier to entry is so high that most 
people who analyze these things are on the bleeding edge anyway, so they 
typically don't need our help. Plus, it somehow never occurred to me to 
build them ;-D

Best,

Jim




> 
> Thanks again.
> 
> Cheers,
> John Woods
> 
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-- 
James W. MacDonald, MS
Biostatistician
UMCCC cDNA and Affymetrix Core
University of Michigan
1500 E Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623