On Tue, Jul 22, 2008 at 6:18 PM, James MacDonald <jmacdon@med.umich.edu>
wrote:

> John wrote:
>
>> 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?).
>

(Yes, of course. And the vignettes.)

I'll try to clarify. Is there a way to tell from the CDF requested in the
CEL which *custom* CDF it should load instead? For example, how do I know
which (of the many CDFs for the Affy 1.0R, 2.0R, 21/22 arrays) custom CDF is
the replacement for the default CDF Wgc_Universal_fe1?


>
> 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)
>

Yes, Google = NSA, and NASA, too. Soon they'll put NAAAAAAAAAASA at the
bottom of search results instead of Goooooooooogle.

So you're saying that instead of calling ReadAffy() with no or few args on
the current working directory, I should call ReadAffy for each CEL
separately, specifying the custom CDF manually? (I guess I was wondering if
there was an option like usecustom=TRUE.)

Trying to increase my understanding:
If I've got three replicates of an array that all come from the same
biological replicate, should those be read in a single call to ReadAffy?



> 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).
>

I'm getting:
package 'affyTiling' is not available.

I do have package tilingArray, but the vignettes there don't really answer
my question. Is there somewhere else I should look? Specifically, I'd like
help on how best to load this data into R using existing (Yoda) methods in
Bioconductor--if it's possible.

The pdInfoBuilder vignette is not terribly helpful either. Is there some
document that explains how all of this stuff gets tied together, and who
should be using which package for what application? I'm really having a
little trouble keeping track.


>
> 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
>

Yay bleeding edge.

Cheers,
John

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