Yes, you are right!
rma(target=()) can be used to collapse to transcript or probeset level.
However, the problem is still there, as I a left with a nice ExpressionSet
obejct that has values mapped to transcripts (if I decide so) but they are
only annotated by something like 4701234. That is a probeset/transcript
name for example. Now that wouldn'T be a problem given that normally such
an identifier could be easily translated via Bioconductors annotation
packages.

But here comes the most significant part: There is no annotation package
available that includes MoEx 1.0 ST identifiers!

I am trying to get my package to work on these Exon arrays. And the package
expects a proper annotation package such as eg. "mouse4302" to be attached
to the annotation slot of the ExpressionSet.

I'm still puzzled.

2012/6/13 cstrato <cstrato@aon.at>

> Dear Andreas,
>
> As Jim already mentioned, package xps is able to preprocess MoExon 1.0 ST
> arrays at the probeset and the gene level, see also my earlier reply to a
> similar question:
> https://www.stat.math.ethz.ch/**pipermail/bioconductor/2012-**
> June/045958.html<https://www.stat.math.ethz.ch/pipermail/bioconductor/2012-June/045958.html>
>
> Best regards
> Christian
> _._._._._._._._._._._._._._._.**_._._
> C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
> V.i.e.n.n.a           A.u.s.t.r.i.a
> e.m.a.i.l:        cstrato at aon.at
> _._._._._._._._._._._._._._._.**_._._
>
>
>
>
> On 6/13/12 4:47 PM, James W. MacDonald wrote:
>
>> Hi Andreas,
>>
>> On 6/13/2012 3:14 AM, Andreas Heider wrote:
>>
>>> Dear mailing list,
>>> I know this was on the list couple of times, and I think I read it
>>> all, but
>>> actually I still don't get it right. So here is my problem:
>>>
>>> I want to be able to work with Mouse Exon 1.0 ST Arrays (NOT Mouse
>>> Gene 1.0
>>> ST) in a similar fashion to eg. HG-U133 arrays.
>>> That means, I want to finally have it accessible as an ExpressionSet
>>> object
>>> with a right Bioconductor annotation assigned. This should include GENE
>>> SYMBOLS, RefSeq IDs and ENTREZ IDs.
>>>
>>
>> The problem here is that you want to do something that AFAIK isn't easy
>> to do. The Gene ST arrays allow you to summarize all the probes that
>> interrogate a particular transcript (e.g., all the exon-level probesets
>> are collapsed to transcript level, and then you summarize). However, for
>> the Exon ST arrays that isn't the case, unless there is something in xps
>> to allow for that - I know next to nothing about that package, so
>> Cristian Stratowa will have to chime in if I am missing something.
>>
>> For the Exon chips, you are always summarizing at the same probeset
>> level, where there are <= 4 probes per probeset, and there can be any
>> number of probesets that interrogate a given exon. Lots of these
>> probesets interrogate regions that aren't even transcribed, according to
>> current knowledge of the genome. When you choose core, extended or full
>> probesets, you are just changing the number of probesets being used, not
>> summarizing at a different level as with the Gene ST chip.
>>
>> So when you say you want gene symbols, refseq ids and gene ids, what
>> exactly are you after? If a given probeset is in the intron of a gene do
>> you want to annotate it as being part of that gene? How about if it is
>> in the UTR (or really close to the UTR)? What do you want to do with the
>> probesets where one or more of the probes binds in multiple positions in
>> the genome? These are all questions that the exonmap package tries to
>> consider, and it gets really complicated. That's why Affy went with the
>> Gene ST chips - they unleashed the Exon chips on us and couldn't sell
>> them because people were saying WTF do I do with this thing?
>>
>> I don't think there is an easy or obvious answer to your question. If
>> you were to come up with what you think are reasonable answers to my
>> questions, then it wouldn't be much work to extract the chr, start, end
>> from the pd.moex.1.0.st.v1 package, and then use GenomicFeatures (e.g.,
>> findOverlaps()) to decide what regions are being interrogated, and
>> annotate from there.
>>
>> Best,
>>
>> Jim
>>
>>
>>
>>> I can import it as a AffyBatch and generate an ExpressionSet with the
>>> help
>>> of the Xmap/exonmap supplied CDF, but there is no annotation attached
>>> to it.
>>>
>>> OR
>>>
>>> I can import the CEL files with the "oligo" package as a Exon Array
>>> object
>>> and generate an ExpressionSet from it.
>>> However in that case it still have no annotation.
>>>
>>> Surprisingly on the Bioconductor website there are all packages needed to
>>> deal with Mouse Gene 1.0 ST arrays but the informtion to work with Mouse
>>> Exon 1.0 ST arrays seems missing!
>>>
>>> What am I doing wrong here? Has someone else had such problems?
>>>
>>> Thanks in advance for your effort,
>>> Andreas
>>>
>>> [[alternative HTML version deleted]]
>>>
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>>>
>>
>>

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